By September 1889, only three years after graduating from the conservatory, Nielsen had progressed well enough on the violin to gain a position with the second violins in the prestigious Royal Danish Orchestra which played at Copenhagen's Royal Theater. This position would sometimes cause Nielsen considerable frustration but he continued to play there until 1905. In between graduation and attaining this position, he gave violin lessons, made a modest income as a teacher and enjoyed continued support from patrons. Some of Nielsen's string chamber works were performed at this time, including a Quartet in F which he considered his official debut as a professional composer. However, the greatest impression was made by the Suite for Strings, which was performed at Tivoli Hall on 8 September 1888. Nielsen would designate this work his Opus 1.

After less than a year at the Royal Theater, Nielsen won a scholarship of 1,800 kroner (£90), giving him the means to spend several months traveling in Europe. During this time he discovered and abandoned Richard Wagner's music dramas, heard many of Europe's leading orchestras and soloists and sharpened his opinions on both music and the visual arts. While revering the music of Bach and Mozart, he remained ambivalent about much 19th century music. In Paris, he met the Danish sculptor Anne Marie Brodersen, who was also traveling on a scholarship. They toured Italy together, marrying in the English Church of St Mark's in Florence on 10 May 1891 before returning to Denmark.

"As well as being a love match," Fanning writes, "it was also a meeting of minds. Anne Marie was a gifted artist.... She was also a strong willed and modern minded woman, determined to forge her own career." This determination would strain the Nielsens' marriage, as Anne Marie would spend months on location during the 1890s and 1900s, leaving Carl to raise their three young children in addition to composing and coping with his duties at the Royal Theater. While Carl suggested divorce in March 1905, the Nielsens remained married for the remainder of the composer's life. Carl sublimated his anger and frustration over his marriage in a number of musical works, most notably between 1897 and 1904, a period to which he sometimes referred as his "psychological" period. Fanning writes, "At this time his interest in the driving forces behind human personality crystallized in the opera Saul og David and the Second Symphony ("De fire temperamenter") and the cantatas Hymnus amoris and Søvnen.

At first, he did not gain enough recognition for his works to be able to support himself. During the concert which saw the premiere of his first symphony on 14 March 1894 conducted by Johan Svendsen, Nielsen played in the second violin section. However, the symphony was a great success when played in Berlin in 1896, contributing significantly to his reputation. Nielsen became increasingly in demand to write incidental music for the theater and cantatas to mark special occasions, both of which provided a welcome source of additional income. "A reciprocal relationship grew up between his programmatic and symphonic works," Fanning writes; "sometimes he would find stageworthy ideas in his supposedly pure orchestral music; sometimes a text or scenario forced him to invent vivid musical imagery which he could later turn to more abstract use."

Beginning in 1901, Nielsen received a modest state pension — 800 kroner at first, growing to 7,500 kroner by 1927 — to augment his violinist's salary. This allowed him to stop taking private pupils and left him more time to compose. From 1903, he also had an annual retainer from his principal publisher, Wilhelm Hansen Edition. Between 1905 and 1914 he served as second conductor at the Royal Theatre. From 1914 to 1926, he conducted the orchestra of Musikforeningen or the Music Society. In 1916, he took a post teaching at the Royal Danish Academy of Music in Copenhagen, and continued to work there until his death, in his last year as director of the institute.

The strain of dual careers and constant separation from his wife led Nielsen to more than one extra - marital affair. When the last one came to light, between Nielsen and his children's governess, the result was an eight year breach in his marriage. During much of this time Carl and Anne Marie lived apart. The period led to a creative crisis for Nielsen, bringing about a powerful reappraisal of himself as a composer. This, along with World War I and professional developments in his life, would strongly influence his Fourth and Fifth Symphonies, arguably his greatest works.

For his son - in - law, the Hungarian violinist Dr. Emil Telmányi, Nielsen wrote his Violin Concerto, Op. 33 (1911).

After suffering a serious heart attack in 1925, Nielsen was forced to curtail much of his activity, although he continued to compose until his death. In 1927, he wrote My Childhood on Funen (Min Fynske Barndom), a delightful memoir of his childhood . He also produced a short book of essays entitled Living Music (1925). Both have been translated into English, and Min Fynske Barndom was made into a docu - drama in 1994. Nielsen died in Copenhagen in 1931.

Nielsen is best known for his six symphonies. Other well known pieces are the incidental music for Adam Oehlenschläger's drama Aladdin, the operas Saul og David and Maskarade, the three concertos for violin, flute and clarinet, the Wind Quintet, and the Helios Overture, which depicts the passage of the sun in the sky from dawn to nightfall. Most Danes can sing many of the numerous songs by various poets, set to music by Carl Nielsen.

The music initially had a neo-classical sound but became increasingly modern as Nielsen developed his own approach to what Robert Simpson called progressive tonality, moving from one key to another. Typically, he would end on a different key, sometimes as the outcome of a struggle as in his symphonies. His frequently blended melodic passages inspired by folk music with more complicated stylings including counterpoint and modern variations.

Like his contemporary, the Finn Jean Sibelius, he studied Renaissance polyphony closely, which accounts for much of the melodic and harmonic "feel" of his music.

Nielsen's works are sometimes referred to by FS numbers, from the 1965 catalogue compiled by Dan Fog and Torben Schousboe.

Nielsen is perhaps most closely associated with his six symphones, which were written between 1892, when he was an aspiring young composer, and 1925, when he was already beginning to suffer from poor health. The works have much in common: they are all just over 30 minutes long, brass instruments are a key component of the orchestration, and they all exhibit unusual changes in tonality, which heightens the dramatic tension.

From its opening bars, Symphony No. 1 in G minor (1890 – 92), while reflecting the influence of Grieg and Brahms, shows Nielsen's individuality. Surprisingly, it begins in C major and hints at what Robert Simpson calls evolving or progressive tonality or the practice of beginning a work in one key and ending in another.The composer, who was playing in the second violins at the work's premiere must have been gratified at the work's highly enthusiastic reception. From his manifestation of personal strength in the First Symphony, in the Second Nielsen embarks on the development of human character. Inspiration came from a painting in an inn depicting the four temperaments (choleric, phlegmatic, melancholic and sanguine). The first and the third movements are reminiscent of the doleful style of Mahler.

The Sinfonia Espansiva is understood by Robert Simpson to mean the "outward growth of the mind's scope". It fully exploits Nielsen's technique of confronting two keys at the same time and includes a peaceful section with soprano and baritone voices, singing a tune without words. Symphony No. 4, "The Inextinguishable", written during the First World War is perhaps the most popular. In the last movement two sets of timpani are placed on opposite sides of the stage as a sort of musical duel. Nielsen described the symphony as "the life force, the unquenchable will to live". Almost as popular is the equally dramatic Fifth Symphony, presenting another battle between the forces of order and chaos. A snare drummer is given the task of interrupting the orchestra, playing ad lib and out of time, with the intention of destroying the music. Performed by the Danish Radio Symphony Orchestra conducted by Erik Tuxen at the 1950 Edinburgh International Festival, it caused a sensation, inspiring interest in Nielsen's music outside Scandinavia. Finally, the Sixth Symphony, written 1924 – 25, is less aurally accessible than the previous five. The tonal language is similar to Nielsen's other symphonies, but the symphony soon degenerates into a number of cameos, some sad, some grotesque, some humorous. Even Robert Simpson was confused.

Nielsen's two operas are in very different styles. The four act Saul og David (Saul and David), written in 1902 to a libretto by Einar Christiansen tells the Biblical story of Saul's jealousy of the young David while Maskarade (Masquerade) is a comic opera in three acts written in 1906 to a Danish libretto by Vilhelm Andersen, based on the comedy by Ludvig Holberg. While Saul og David is one of Denmark's most important musical works for the theatre, it is difficult to stage as the really dramatic episodes are often separated by longer, less dynamic sequences. The choral scenes are certainly among the opera's highlights. The music, which is both dramatic and lyrical, is free of any late Romantic effects. The much lighter Maskarade, on the other hand, is considered to be Denmark's national opera as a result of its lasting success and popularity. Its many strophic songs and wonderful dances have great appeal for Danish audiences as has its underlying "old Copenhagen" atmosphere. The ensembles such as the striking wind quartet at the end of the first act are full of life while the orchestration is the most balanced in all of Nielsen's works.

Nielsen wrote a considerable number of choral works but most of them were composed for special occasions and were seldom repeated. Three fully - fledged cantatas for soloists, orchestra and choir have, however, become part of the modern repertoire. Hymnus amoris (Hymn of Love) (1897) is inspired by Titian's painting "The Miracle of a Jealous Husband" which Nielsen saw on his honeymoon in Italy in 1891. On one of the copies, Nielsen wrote: "To my own Marie! These tones in praise of love are nothing compared to the real thing." Nielsen composed the work after studying the choral style of the old polyphonic masters. Its premiere at the Music Society in April 1897 was a great success. Søvnen (The Sleep), Nielsen's second major choral work, sets to music the various phases of sleep including the terror of a nightmare in its central movement which, with is unusual discords, came as an unwlecome shock to the reviewers at its premiere in March 1905. Fynsk Foraar (Springtime on Funen), completed in 1922, is often cited as the most Danish of all Nielsen's compositions as it extols the beauty of Funen's countryside.

Nielsen wrote three concertos: the Violin Concerto is a mature work, from 1911, which lies within the tradition of European classicism, whereas the Flute Concerto of 1926 and the Clarinet Concerto which followed in 1928 are late works, influenced by the modernism of the 1920s and the product of "an extremely experienced composer who knows how to avoid inessentials." Unlike Nielsen's later works, the Violin Concerto has a distinct, melody oriented Neo-Classical structure. Unusually, there are three movements. The calm "Praeludium" is followed by a catching tune for the orchestra providing opportunities for tricks by the violin. The long, slow Adagio leads to the final Scherzo which, as Nielsen commented, "renounces everything that might dazzle or impress." The Flute Concerto was written for the flautist Holger Gilbert - Jespersen, a member of the Copenhagen Wind Quintet who had performed in Nielsen's Wind Quintet (1922). In contrast to the rather traditional style of the Violin Concerto, it reflects the modernistic trends of the 1920s. The first movement, for example, switiches between D minor, E flat minor and F major before the flute comes to the fore with a cantabile theme in E major. Similarly, the Clarinet Concerto was specifically written for a member of the Copenhagen Wind Quintet, namely the clarinetist Aage Oxenvad. Nielsen seems to have had an uncanny understanding of the clarinet, stretching its abilities to the utmost. Unusually, the Clarinet Concerto has just one continuous movement and contains a struggle between the soloist and the orchestra and between the two principal competing keys, F major and E major.

The Helios Overture (1903) stems from Nielsen's stay in Athens which gave him the inspiration of a work depicting the sun rising and setting over the Aegean Sea. The score is written for three flutes, two oboes, two clarinets, two bassoons, four horns, three trumpets, three trombones, tuba, timpani, and strings. A great showpiece for orchestra, it has been one of Nielsen's most popular works ever since. Saga - Drøm (Saga Dream), sometimes known as Gunnar's Dream, is a tone poem for orchestra based on the Icelandic Njal's Saga. In Nielsen's words: "There are among other things four cadenzas for oboe, clarinet, bassoon and flute which run quite freely alongside one another, with no harmonic connection, and without my marking time. They are just like four streams of thought, each going its own way — differently and randomly for each performance — until they meet in a point of rest, as if flowing into a lock where they are united."

At the Bier of a Young Artist (Ved en ung Kunstners Baare) for string orchestra was written for the funeral of the Danish painter Oluf Hartmann in January 1910. The four minute piece in E flat minor was first performed by the Gade Quartet at Oluf Hartmann’s funeral on 21 January in the chapel at Holmen’s Cemetery in Copenhagen and was also played at Nielsen's own funeral. Pan and Syrinx (Pan og Syrinx), a vigorous nine minute symphonic poem inspired by Ovid's Metamorphoses, was particularly well received at its premiere in 1911, Charles Kjerulf of Politken commenting: "For each note that was added it became more and more sublime."

The Rhapsodic Overture, An Imaginary Trip to the Faroe Islands (En Fantasirejse til Færøerne), is an occasional work which depicts a sea voyage from Denmark to the Islands. It draws on Faroese folk tunes but also contains freely composed sections.

Among Nielsen's orchestral works for the stage are Aladdin (1919) and Moderen, Opus 41 (1920). Aladdin was written to accompany a production of Adam Oehlenschläger’s fairy tale at The Royal Theatre in Copenhagen. The complete score, lasting over 80 minutes, is Nielsen's longest work apart from his operas but is now often performed as the shorter orchestral suite consisting of the Oriental March, Hindu Dance and Negro Dance. Moderen, written to celebrate the reunification of Southern Jutland with Denmark, was first performed on 30 January 1921 at the Royal Danish Theatre where it was well received. The text was basically a collection of generally patriotic verses written by Helge Rode for the occasion.

Nielsen composed a number of chamber music works, some of them still high on the international repertoire. The Wind Quintet, one of his most popular pieces, was composed in 1922 specifically for the Copenhagen Wind Quintet. Robert Simpson writes, "Nielsen’s fondness of wind instruments is closely related to his love of nature, his fascination for living, breathing things. ... He was also intensely interested in human character, and in the Wind Quintet composed deliberately for five friends; each part is cunningly made to suit the individuality of each player."

The Fantasy Pieces for Oboe and Piano (Fantasistykker for obo og klavier) consists of two pieces which were first performed at the Royal Orchestra Soirée in Copenhagen on 16 March 1891. The oboist was Olivo Krause (to whom they are dedicated) and the pianist Victor Bendix. Transcriptions by Hans Sitt for violin and piano and for violin and orchestra have also remained popular. Nielsen's four string quartets are all part of the current repertoire. The First String Quartet No. 1 in G minor (1889) was innovative in the "Résumé" section which Nielsen included in the finale, bringing together themes from the first, third and fourth movements. The Second String Quartet No. 2 in F minor (1890) provides evidence of Nielsen's early experiments with tonality. The Third String Quartet in E flat major (1898) has remained one of Nielsen's more popular works, particularly in Denmark. The Fourth String Quartet in F major (1904) was initially criticised by the reviewers but is now recognised for its innovative approach.

Although Nielsen came to compose mainly at the piano,  he only composed directly for it occasionally over a period of 40 years, creating five major works and several others, often with a distinctive style which slowed their international acceptance. One of his most successful compositions for piano is Chaconne, Opus 32, which Nielsen qualified as "a really big piece, and I think effective". It was premiered by Alexander Stoffregen on 13 April 1917 and was generally well received by its reviewers. On 11 February 1918, Christian Christiansen received an ovation when he played the piece during a concert of Nielsen’s orchestral works. Charles Kjerulf described the work as "a genuine Carl Nielsen piano - experiment".

All Nielsen's organ works were late compositions. Danish organist Finn Viderø suggests that this reflects the relative neglect of the organ during most of his life. This situation changed with the Orgeltagung (Organ Meeting) in Hamburg organised by Hans Henny Jahnn in 1925, which was a major stimulus for the Orgelbewegung (Organ reform movement), and the renewal of the front pipes of the Schnitger organ in the St. Jacobi Church by Karl Kemper from 1928 – 1930. Nielsen's last major work, Commotio, Opus 58, a 22 minute piece for organ, was composed between June 1930 and February 1931. The composer considered it to be one of his most important works.

Over the years, Nielsen wrote the music for over 290 songs and hymns, most of them for poems written by well known Danish authors such as N.F.S. Grundtvig, B.S. Ingemann, Poul Martin Møller, Adam Oehlenschläger and Jeppe Aakjær. In Denmark, many of them are still popular today, both with adults and children. Among the more popular ones are Farvel min velsignede Fødeby! (1914), Havet omkring Danmark (1907), Hvem sidder der bag Skjærmen (Jens Vejmand) (1907), Jeg ved en Lærkerede (c. 1924), Op al den Ting, som Gud har gjort' (c. 1914), Som en rejselysten Flaade (1921), Spurven sidder stum bag Kvist (1914) and Vi Sletternes Sønner har Drømme i Sind (1908).