In the Extended Finale, BoBoiBoy leaves Rintis Island. But, after 6 months later, he came back to Rintis Island and studied at Rintis Island Primary School along with his friends. This season focuses mainly on the adventures that BoBoiBoy and his friends have at Rintis Island Primary School.
- The episodes still don't have official titles.
- The scene where BoBoiBoy hugged Tok Aba is seen again (Episode 1).
- Unlike in the first season, Nizam Razak was replaced by Yap Ee Jean and Dzubir Mohammed Zakaria as the directors of the series.
- In Season 1, BoBoiBoy was wearing two Power Bands. While in Season 2, he has only one.
- In Episode 1, Yaya said that Tok Aba is really lucky to have a grandson like BoBoiBoy which is almost the same in the pilot episode when BoBoiBoy said that he is lucky to have a granddad like Tok Aba.
- Season 2 episodes running time is 21 minutes unlike Season 1, which is 11 minutes in each episode.
- From Episode 12, both Team Adu Du and Team BoBoiBoy have united together to stop Ejo Jo for threatening the Earth.
- Fang - (voiced by Wong Wai Kay): Known as the "Mystery Boy" (Budak Misteri) in the Extended Finale. As a new character in the series he is jealous of BoBoiBoy (so are Adu Du and Probe) because all of his classmates likes BoBoiBoy more than him. From Episode 4 onwards, Adu Du and Probe became friends with him.
- Teacher Timmy - (voiced by Fatimah Zafira): As an English Teacher and 5th Grade Section Jujur (Honest) adviser of Rintis Island Primary School.
- Ejo Jo - (voiced by Noriman Saffian): An alien who's the General Commander of the Planet Ata Ta Tiga.
- Iwan - (voiced by Nurasyikin "Ekeen" Khalit): He joined Team BoBoiBoy (Soccer Game) in the Soccer game against Team Adu Du (Soccer Game) if it wasn't for him Team BoBoiBoy would have been defeated. And his one of BoBoiBoy's classmates.
|No. in Series||No. in Season||Episodes Title||TV3 Air Date|
|14||1||"The Return of BoBoiBoy"||May 27, 2012|
|15||2||"The Haunted House"||June 3, 2012|
|16||3||"BoBoiBoy Vs. Fang"||June 10, 2012|
|17||4||"The Football Game"||June 24, 2012|
|18||5||"The Revenge of Adu Du"||August 26, 2012|
|19||6||"Tiny Boys"||September 9, 2012|
|20||7||"Uncontrollable Emotions"||December 9, 2012|
|21||8||"Fang's Past"||December 16, 2012|
|22||9||"Battle for the Underground/MKHIPI"||December 23, 2012|
|23||10||"Close Encounters"||December 30, 2012|
|24||11||"The Math Test"||March 10, 2013|
|25||12||"Battle of Ejo Jo"||March 17, 2013|
|26||13||"Battle of Ejo Jo Part 2"||March 24, 2013|