His Highness was the son of Sultan Muhammad Jamalul Alam I and Raja Isteri Pengiran Anak Nur Alam. He was the grandson of two Sultans of Brunei, Muhammad Tajuddin and Muhammad Kanzul Alam.
Succession to the throne
When his father died in 1804, he was still a minor. Therefore, his grandfather, Paduka Seri Bega'wan Muhammad Tajuddin ascended the throne for the second time. Due to the advanced age of Sultan Muhammad Tajuddin, his younger brother, Pengiran Di-Gadong Pengiran Muda Muhammad Kanzul Alam acted as regent. When Sultan Muhammad Tajuddin died in 1807, the regent became the 21st Sultan of Brunei and was known as Sultan Muhammad Kanzul Alam. Sultan Muhammad Kanzul Alam then appointed his own son, Pengiran Anak Muhammad Alam as heir to the throne of Brunei. In 1825, when Pengiran Muda Omar Ali Saifuddin had come of age, he asserted his claim to the throne. Pengiran Muda Omar Ali Saifuddin was supported by most nobles as he was the rightful heir according to Brunei’s royal traditions. The :it:Kris Si Naga|Kris Si Naga was in the possession of his mother, thus strengthened his claim. To end the succession crisis, Sultan Muhammad Alam stepped down from the throne and was sentenced to death. In 1828, Pengiran Muda Omar Ali Saifuddin ascended the throne as the 23rd Sultan of Brunei, taking the title Sultan Omar Ali Saifuddin II.
Reign
During Sultan Omar Ali Saifuddin II’s reign, he tried to establish absolute control over Sarawak. Before this, only the Pengirans who acted on behalf of the Sultan, were in charge in Kuching collecting taxes and revenues from the local people. Especially after the discovery of antimony ore in Sarawak, the Sultan became more ambitious in gaining control of the economy of Sarawak. The Governor of Sarawak at that time, Pengiran Indera Mahkota Mohammad Salleh, also used forced labour to run the antimony mines. A disturbance occurred in Sarawak where an uprising against Brunei rule led by :it:Datu Patinggi Ali|Datu Patinggi Ali, who was one of the ruling chiefs in Sarawak.
James Brooke
At the time of chaotic situation in Sarawak, an explorer, James Brooke came to Sarawak. Brooke came to Sarawak from Singapore as he had heard about Sarawak's economic potentials. Also, at this time, Brooke met the Prime Minister :it:Pengiran Muda Hashim|Pengiran Muda Hashim, who was the uncle of Sultan Omar Ali Saifuddin II, and the two became close friends. Pengiran Muda Hashim asked for Brooke's assistance to help him to crush the disturbances in Sarawak, in return, Pengiran Muda Hashim ensured the appointment of Brooke as the new Governor of Sarawak, after the current Governor Raja :it:Indera Mahkota|Pengiran Indera Mahkota deposed. There is no clear reason why Brooke later accepted Pengiran Muda Hashim's offer. After the disturbances in Sarawak successfully quelled, James Brooke met Pengiran Muda Hashim in Kuching to ensure his promises were kept. Pengiran Muda Hashim was left with no choice. In 1842, Sultan Omar Ali Saifuddin II confirmed the appointment of James Brooke as the Governor of Sarawak. In 1846, Brunei Town was attacked and captured by the British and Sultan Saifuddin II was forced to sign a treaty to end the British occupation of Brunei Town. The treaty officially recognised James Brooke as the Raja of Sarawak and the Sultan had to cede Sarawak to James Brooke. The loss of Kuching to Brooke marked the beginning of further loss of territories to James Brooke and later, the British North Borneo Company. In the same year, His Highness ceded Labuan to the British under the Treaty of Labuan.
In 1847, Sultan Omar Ali Saifuddin II signed the Treaty of Friendship and Commerce with the British and in 1850, he signed a similar treaty with the United States.
Death
The cession of Sarawak to James Brooke and Labuan to Great Britain, had a major effect on the Sultan whose health immediately deteriorated after that. The Sultan chose to distance himself from ruling the state but he never abdicated the Throne. At the moment, his son-in-law Abdul Momin was appointed a regent. Omar Ali Saifuddin II died in 1852 and was succeeded by his son-in-law, Sultan Abdul Momin as the 24th Sultan of Brunei. He was buried at Kubah Makam Di Raja or the Bukit Penggal Royal Mausoleum, Bandar Seri Begawan.