The town of Apatou was founded in 1882 as Moutendé.[3] It was renamed after Captain Apatou of the Aluku.[4] In the late 19th century, Apatou was a guide for the explorer Jules Crevaux. On 7 September 1885, Jules Brunetti opened a Catholic mission in the village.[5] In 1891, Apatou mediated between France and the Colony of Suriname with regards to the border, and allied the Aluku with France.[4] He also united all the different tribes on the French side.[3]
Apatou was up to 1969 part of the Inini territory which allowed for an autonomous and self sufficient tribal system for the Maroons without clear borders.[6] Along with the commune, came a government structure, and francisation. Most importantly, it led to the concentration in bigger villages and the near abandonment of smaller settlements.[6]
The commune of Apatou was created on 12 November 1976 by detaching its territory from the commune of Grand-Santi-Papaichton (since then renamed Grand-Santi).[3]
The villages in the commune could only to be reached by boat from the Maroni River.[3] In 2010, Route Nationale opened connecting Apatou with Saint-Laurent-du-Maroni, and the road network of French Guiana. The road was opened with the Tour of Guiana.[8] The road is scheduled to be extended to Maripasoula. Construction work on the section to Papaïchton is planned to begin in 2021.[9]