The third season consists of 26 episodes, originally airing from August 2013 to June 2016.

In this season, BoBoiBoy defeats Ejo Jo, and Adu Du bin Abu Seman becomes BoBoiBoy's friend but he turns evil back again because of his mother. Boboiboy also gets his new Fire and Water Elemental powers.

This is the first season that new episodes would be uploaded onto YouTube before its first airing on TV. It is also the first season to change the theme song, switching out "BoBoiBoy Superhero Kita" (English: BoBoiBoy, Our Superhero!) with "Jagalah Bumi" by Kotak.