Gojong took the throne in 1863 when he was still a child. His father, Regent Heungseon Daewongun, ruled for him until Gojong reached adulthood.

During the mid 1860s Heungseon Daewongun was the main proponent of isolationism and the instrument of the persecution of native and foreign Catholics, a policy that led directly to the French Campaign against Korea, 1866, United States expedition to Korea in 1871. The early years of Heungseon Daewongun's rule also witnessed a large effort to restore the largely dilapidated Gyeongbok Palace, the seat of royal authority. During Heungseon Daewongun's reign, faction politics, Seowon and power wielded by the Andong Kim clan completely disappeared.

In 1873, He announced the direct royal rule. With the retirement of Heungseon Daewongun, the to-be Queen Min (Later called Empress Myeongseong) gained complete control over her court, placing her family in high court positions.

In the 19th century tensions mounted between Qing China and Japan, culminating in the First Sino - Japanese War (1894 – 1895). Much of this war was fought on the Korean peninsula. Japan, after the Meiji Restoration, acquired Western military technology, had forced Joseon to sign the Treaty of Ganghwa in 1876. Japan encroached upon Korean territory in search of fish, iron ore, and natural resources. It also established a strong economic presence in the peninsula, heralding the beginning of Japanese imperial expansion in East Asia.

The French campaign against Korea of 1866, United States expedition to Korea in 1871 and the Incident of Japanese gunboat Unyo put pressure on many of Joseon's officers including King Gojong.

The Treaty of Ganghwa became the first unequal treaty signed by Korea; it gave extraterritorial rights to Japanese citizens in Korea, forced the Korean government to open three ports to Japanese and foreign trade, Busan, Incheon and Wonsan, and established Korean independence from China, building the Dongnimmun (독 립문, or "Independence") Gate in commemoration. Korea had until this point paid regular tribute to China with the delivery of sums of money, Korean kings first had to be approved by China, and at various times Korea considered itself culturally descended from China, although China would customarily reciprocate to these tributes with gifts of equal value and the Chinese generally rubber - stamped any candidate proposed for king in Korea . Thus establishing independence was to some extent just political phrasing. Nevertheless, by driving a political wedge, whether perceived or real, between Korea and China, Japan effectively made it more difficult for Korea to seek Chinese military assistance.

King Gojong began to rely on newer, rifle using armies. They were paid well and the old army who used spears and old matchlocks lost much of their pay. The old army revolted after receiving mediocre wages. Heungseon Daewongun was restored to power, But the Qing general, Yuan Shikai soon had the Daewongun abducted by Chinese troops and taken to China, thus foiling his return to power. Four years later the Daewongun returned to Korea.

On 4 December 1884, 5 revolutionaries led a small anti-old minister army to Empress Myeongseong's brother's house and initiated a coup d'etat. It failed in 3 days. Some Coup leaders, including Kim Okgyun, fled to Japan, and others were executed.

Widespread poverty presented significant challenges to the 19th century Joseon Dynasty. One indication of this poverty was the average life expectancy of Koreans around the close of the Joseon period: 24 years for males and 26 for females. A number of factors, including famine, poverty, high taxes and corruption among the ruling class led to several notable peasant revolts in the 19th century. King Gojong's predecessors had suppressed an 1811 - 1812 revolt led by Hong Kyong-nae in the Pyeongan Province. In 1894, another major revolt, the Donghak Peasant Revolution took hold as an anti-government, anti-yangban and anti-foreign campaign. To suppress the rebellion, the Joseon government requested military aid from Japan, thus deepening Japanese claims to Korea as a protectorate. In the end, the revolution failed, but many grievances of the peasants would later be addressed through the Gabo Reform.

In 1895, Empress Myeongseong (referred to as "Queen Min" by the Japanese) was assassinated by Japanese agents. The Japanese minister to Korea, Miura Goro orchestrated the plot against her. A group of Japanese agents entered the Imperial palace in Seoul, which was under Japanese guard, and Empress Myeongseong was killed in the North wing of the palace. The empress had attempted to counter Japanese interference in Korea and was considering turning to Russia or China for support.

Meanwhile, Japan won the Sino - Japanese War (1894 – 1895), gaining much more influence on the Korean government. Also the Gabo reforms and Assassination of Empress Myeongseong stirred controversy in Korea along with anti - Japanese sentiments.

Some Confucian scholars, as well as farmers, formed over 60 successive righteous armies to fight for Korean freedom. These armies were preceded by the Donghak movement and succeeded by various Korean independence movements.

On 11 February 1896, King Gojong and his crown prince fled from the Gyeongbokgung palace to the Russian legation in Seoul, from which they governed for about one year, an event known as Korea royal refuge at the Russian legation.

In 1897, King Gojong, yielding to rising pressure from both overseas and the demands of the Independence Association led public opinion, returned to Gyeongungung (modern day Deoksugung). There, he proclaimed the founding of the Empire of Korea, officially redesignated the national title as such, and declared the new era name Gwangmu (Hangul: 광무, Hanja: 光武) (meaning shining warrior), effectively severing Korea's historic ties to the Qing Chinese tradition which Korea had adhered to since the fall of the Ming Dynasty, and turning King Gojong into the Gwangmu Emperor, the first imperial head of state and hereditary sovereign of the Empire of Korea. This marked the complete end of the old world order and traditional Chinese tributary system in the Far East, where the status of empire meant independence from Qing dynasty China as with all of its predecessors, and also, at least nominally, implemented the "full and complete" independence of Korea as recognized in 1895.

Gojong proclaimed the Korean Empire in 1897 to justify its independence from tributary status of China. He tried to promote the ultimately unsuccessful Gwangmu Reform.

The Japanese military consistently attained victory in the Russo - Japanese War (1904 – 1905). Following the Protectorate Treaty of 1905 between Korea and Japan, which stripped Korea of its rights as an independent nation, he sent representatives to the Hague Peace Convention of 1907 in order to try to re-assert his sovereignty over Korea. Although the Korean representatives were blocked by the Japanese delegates, they did not give up, and later held interviews with newspapers.

One representative warned forebodingly of Japanese ambitions in Asia: "The United States does not realize what Japan's policy in the Far East is and what it portends for the American people. The Japanese adopted a policy that in the end will give her complete control over commerce and industry in the Far East. Japan is bitter against the United States and against Great Britain. If the United States does not watch Japan closely she will force the Americans and the English out of the Far East."

As a result, Gojong was forced to abdicate by the Japanese and Gojong's son, Sunjong succeed to the throne.

After abdicating, Emperor Gojong was put in the Deoksu Palace confinement by the Japanese. On 22 August 1910, the Empire of Korea was annexed by Japan with the Japan - Korea Annexation Treaty.

He died on 21 January 1919 in Deoksugung. There is much speculation that he was killed by poison that was administered by Japanese officials. He is buried with his wife at the imperial tomb of Hongneung (홍릉, 洪陵) in the city of Namyangju.