Semporna was founded soon after the British North Borneo Chartered Company established Sandakan, and initially settled by Chinese traders, most fleeing from Spanish attacks on the Sulu Sultanate.

Before being named "Semporna", this area was known as "Tong Talun" in Bajau language which means "Hujung Hutan" in Malay or "at the end of the forest" in English.

[2] Including other parts of eastern Sabah, this area was ruled by the Sultanate of Sulu before being handed over to the British North Borneo Chartered Company in 1876 by agreement.

[2] Action by Sir James Brooke, and other western colonial powers such as the Dutch and Spanish, managed to successfully combat the pirates over the course of the 1800s.

[2] Upon the advent of the Chartered Company in the early 1880s, only one pirate stronghold remained at Omadal island, which was defeated by HMS Zephyr in 1886.

[2] With pirates having recently destroyed the settlement of Maimbung in Sulu, some of the Chinese merchants there asked for permission to settle in the Company's territory, under the rule of law and its resulting security.

[2] Semporna was the site of a small-scale migration of Chavacano speakers from Zamboanga, fleeing the Malaysia-funded Moro Conflict between Muslim rebels and the Philippine government.

These Chavacanos speak a Creole of Mexican-Spanish[4] and are partially descended from Peruvian settlers mixed with indigenous Filipinos[5] from the former Rajahnate of Sanmalan.

They are one of the few nomadic seaborne peoples of the world, and spend most of their lives on boats, making a livelihood from the coral reefs in the area.