When the Tswana tribes first moved in to the region in about the 1800s, they discovered hot springs in the area.
The Voortrekker Carl Van Heerden established the first farm in what is now Bela-Bela and called it Het Bad. In 1873, President Burger's Transvaal government bought the land and established a resort called Hartingsburg after the prominent Dutch biologist Pieter Harting. The British occupied the town during the Anglo Boer War, and renamed the post office Warm Baths in 1903, and proclaimed the boundaries of Warmbaths to be the entire farm of Het Bad.
In 1920 Warmbaths was proclaimed a township (in the legal, not racial sense) and the township was designed by architect John Abraham Moffat in that year. In 1950, it became a magisterial district. In 1932 Warmbaths became a village town and got a town council in 1960.
On 14 June 2002 the South African government officially renamed the town to Bela-Bela (meaning "boiling boiling") .
Incorrect variations on this spelling can also be sometimes found, such as "Bella Bella" and "Bela Bela"