Henry was born at the Royal Château de Fontainebleau, Seine-et-Marne, fourth son of King Henry II and Catherine de' Medici, grandson of Francis I of France and Claude of France, and brother of Francis II of France and Charles IX of France. He was made Duke of Angoulême and Duke of Orléans in 1560, and Duke of Anjou in 1566. In 1564, his name became Henri. He was his mother's favourite; she called him chers yeux ("Precious Eyes") and lavished fondness and affection upon him for most of his life. His elder brother, Charles, grew to detest him, resenting Henry's greater health and activity. In his youth, he was considered the best of the sons of Catherine de' Medici and Henry II. Unlike his father and elder brothers, he had little interest in the traditional Valois pastimes of hunting and physical exercise. Although he was both fond of fencing and skilled in it, he preferred to indulge his tastes for the arts and reading. These predilections were attributed to his Italian mother.

At one point in his youth he showed a tendency towards Protestantism as a means of rebelling. At the age of nine, calling himself un petit Huguenot, he refused to attend Mass, sang Protestant psalms to his sister Margaret (exhorting her all the while to change her religion and cast her Book of Hours into the fire), and even bit the nose off a statue of Saint Paul. His mother firmly cautioned her children against such behaviour, and he would never again show any Protestant tendencies — instead becoming nominally Roman Catholic.

It has long been claimed that Henry was homosexual or at least bisexual. The scholar Louis Crompton provides substantial contemporary evidence of Henry III's homosexuality, and the associated problems at court and politics. Despite this, it is still disputed. For example, some modern historians, such as P. Erlanger, J.F. Solnon, Nicolas Le Roux, and J. Boucher found evidence to support the idea that Henry was not homosexual (though still perhaps bisexual), but he had many famous mistresses. They found that there were no men named with whom he could have had sex, and that he was well known at the time for his taste in beautiful women. They concluded that his supposed homosexuality was based on his dislike of war and hunting being interpreted as effeminate, an image cultivated by political opponents (both Protestants and ultra-Catholics) to turn the opinion of the French people against him.

In 1570, discussions commenced to arrange for Henry to court Elizabeth I of England. Elizabeth, almost 37, was in need of a husband in order to produce an heir. However, nothing came of these discussions. Elizabeth is viewed by historians as having intended only to arouse the concern of Spain, rather than to have seriously contemplated marriage. The chance of marriage was further blighted by their differing religious views — Henry was at least formally a Catholic while Elizabeth was a Protestant — and his opinion of Elizabeth. Henry tactlessly referred to Elizabeth as a putain publique (a "public whore") and made stinging remarks about their difference in age. Upon hearing (inaccurately) that she limped because of a varicose vein, he called her an "old creature with a sore leg".

Prior to ascending the throne, he was a leader of the royal army in the French Wars of Religion against the Huguenots, and took part in the victories over them at Battle of Jarnac and Battle of Moncontour. While still Duke, he was involved in the plot for the St. Bartholomew's Day Massacre (but did not participate), in which thousands of Huguenots were killed; his reign as King, like the ones of his elder brothers Francis II and Charles IX, would see France in constant turmoil over religion.

Henry continued to take an active role in the French Wars of Religion, and in 1572 - 1573 led the Siege of La Rochelle, a massive military assault on the Huguenot held city of La Rochelle by Catholic troops during the fourth phase of the French Wars of Religion. At the end of May 1573, Henry learned that he had been elected King of Poland, a country with a large Protestant minority, and political considerations forced him to negotiate an end to the assault. An agreement was reached on 24 June 1573 and Catholic troops ended the siege on 6 July 1573.

In 1573, following the death of the Polish ruler Sigismund II Augustus, Jean de Monluc was sent as the French envoy in Poland to negotiate the election of Henry of Valois, future Henry III of France, on the Polish throne, in exchange for military support against Russia, diplomatic assistance in dealing with the Ottoman Empire, and financial help. On 16 May 1573 Polish nobles elected Henry, as the first elected monarch of the Polish - Lithuanian Commonwealth. However, the Lithuanian nobles boycotted this election, and it was left to the Lithuanian ducal council to confirm his election. Thus the Commonwealth elected Henry, rather than Habsburg candidates, partly in order to be more agreeable to the Ottoman Empire (a traditional ally of France through the Franco - Ottoman alliance), and thereby strengthening a Polish - Ottoman alliance which was also in effect.

A Polish delegation went to La Rochelle to meet with Henry who was leading the Siege of La Rochelle (1572 – 1573). Henry left the siege following their visit. In Paris, on 10 September, the Polish delegation asked Henry to take an oath, at Notre Dame Cathedral, to "respect traditional Polish liberties and the law on religious freedom that had been passed during the interregnum". As conditions for his free election, he was compelled to sign the pacta conventa and the Henrician Articles, pledging religious tolerance in the Polish - Lithuanian Commonwealth. Henry chafed at the restrictions on monarchic power under the Polish - Lithuanian political system of "Golden Liberty". The Polish - Lithuanian parliament had been urged by Anna Jagiellon, the sister of the recently deceased king Sigismund II Augustus, to elect him based on the understanding that Henry would wed Anna afterward.

It was at a ceremony before the Paris parlement on 13 September that the Polish delegation handed over the "certificate of election to the throne of Poland - Lithuania". Henry also gave up any claims to succession and he "recognized the principle of free election" under the Henrician Articles and the pacta conventa.

It was not until January 1574 that Henry was to reach the borders of Poland. On 21 February, Henry's coronation was held. It was in mid June 1574 that Henry would take leave of Poland and head back to France, upon hearing of his brother, Charles IX's death. Henry's absence 'provoked a constitutional crisis' which Parliament attempted to resolve by notifiying Henry that his throne would be lost if he did not return from France by 12 May 1575. His failure to return caused Parliament to declare his throne vacant.

The short reign of Henry at Wawel Castle in Poland was marked by a clash of cultures between the Polish and the French. The young king and his followers were astonished by several Polish practices and disappointed by the rural poverty and harsh climate of the country. The Polish, on the other hand, wondered if all Frenchmen were as concerned with their appearance as their new King appeared to be. In many aspects, Polish culture had a positive influence on France. At Wawel, the French were introduced to new methods of septic facilities, in which litter (excrement) was taken outside the castle walls. On returning to France, Henry ordered the construction of such facilities at the Louvre and other palaces. Other inventions introduced to the French by the Polish included a bath with regulated hot and cold water and the fork.

His brother, Charles IX of France, died three months after Henry's coronation as king of the Polish - Lithuanian Commonwealth and Henry secretly departed and returned to France. Henry was crowned king of France on 13 February 1575, at Reims Cathedral. Although he was expected to produce an heir after he married Louise of Lorraine (14 February 1575), they were unable to conceive a child.

In 1576, Henry signed the Edict of Beaulieu, granting many concessions to the Huguenots. His action resulted in the Catholic activist, Henry I, Duke of Guise, forming the Catholic League. After much posturing and negotiations, Henry was forced to rescind most of the concessions that had been made to the Protestants in the Edict of Beaulieu.

In 1584, the King's youngest brother and heir presumptive, Francis, Duke of Anjou, died. Under Salic Law, the next heir to the throne was Protestant Henry III of Navarre, a descendant of St. Louis IX. Under pressure from the Duke of Guise, Henry III issued an edict suppressing Protestantism and annulling Henry III of Navarre's right to the throne.

Henry began a great friendship with the Feuillant reformer Jean de la Barrière and built a monastery for him and his followers to commemorate their friendship in 1587.

On 12 May 1588, when Henry I, Duke of Guise, entered Paris, Henry III fled the city. On 23 December 1588, at the Château de Blois, the Duke of Guise arrived in the council chamber where his brother Louis II, Cardinal of Guise, waited. The Duke was told that the King wished to see him in the private room adjoining the royal bedroom. There guardsmen murdered the Duke, then the Cardinal. To make sure that no contender for the French throne was free to act against him, the King had the Duke's son imprisoned. Henry I, Duke of Guise, had been highly popular in France, and the citizenry turned against King Henry for the murders. The Parlement instituted criminal charges against the King, and he joined forces with his heir, the Protestant Henry of Navarre, setting up the Parliament of Tours.

Under Henry, France named the first Consul of France in Morocco, in the person of Guillaume Bérard. The request came from the Moroccan prince Abd al-Malik who had been saved by Bérard during an epidemic in Constantinople, and wished to retain Bérard in his service.

On 1 August 1589, Henry III lodged with his army at Saint-Cloud, Hauts-de-Seine, prepared to attack Paris, when a young fanatical Dominican friar, Jacques Clément, carrying false papers, was granted access to deliver important documents to the King. The monk gave the King a bundle of papers and stated that he had a secret message to deliver. The King signaled for his attendants to step back for privacy, and Clément whispered in his ear while plunging a knife into his abdomen. Clément was killed on the spot by the guards. At first the King's wound did not appear fatal, but he enjoined all the officers around him, in the event that he did not survive, to be loyal to Henry of Navarre as their new king. The following morning — the day that he was to have launched his assault to retake Paris — Henry III died.

Chaos swept the attacking army, most of it quickly melting away; the proposed attack on Paris was postponed. Inside the city, joy at the news of Henry III's death was near delirium; some hailed the assassination as an act of God.

Henry III was interred at the Saint Denis Basilica. Childless, he was the last of the Valois kings. Henry III of Navarre succeeded him as Henry IV, the first of the Bourbon kings. During the French Revolution he was disinterred from his tomb, his body being desecrated and thrown into a common grave.