The second season consists of 13 episodes, it was aired on Sunday, 27 May 2012 at 7:00 pm on TV3.

In this season, BoBoiBoy begins a new chapter of his life as he moves to Pulau Rintis to reunite with Tok Aba Bin Abah Kau, Gopal, Ying and Yaya. The story in this season mainly centres on BoBoiBoy and his friends' life at Pulau Rintis Primary School. BoBoiBoy also encounters a new challenger, Fang at his new school.

Fang or Mystery Boy was first introduced in Season 1 on Extended Finale episode. In Season 2 finale BoBoiBoy's friends along with Fang fight a super-powerful alien named Ejo Jo who takes all the power watches except for Fang and Boboiboy, and to defeat him, Fang uses his full power.