Season 1 of BoBoiBoy premiered on March 13, 2011.

The first season of consists of 13 episodes and one special extended finale episode. It started airing on Sunday, 13 March 2011 at 7:00 pm on TV3. It was shown on Disney Channel Asia starting 11 June 2011, and on NTV7 starting 24 May 2014.

The episode starts with the main character, BoBoiBoy on a trip to his grandfather Tok Aba's home in Pulau Rintis for the school holidays. At the same time, Adu Du, an alien from the planet of Ata Ta Tiga heads to Earth, to search for energy resources. He finds out that there is cocoa, a powerful energy source, which had extinct from his planet about 30,000 years ago. Adu Du wanted to conquer all the cocoa for himself so that he could be a hero for his planet. To make sure his plan succeeded, he sought help from the Power Sphere (Ochobot). However, a series of mishaps occur and BoBoiBoy obtains Ochobot instead. Ochobot then gives some superpowers to BoBoiBoy and his new friends, Ying, Yaya and Gopal.

Season 2 of BoBoiBoy premiered on May 27, 2012.

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.

Season 3 of BoBoiBoy premiered on August 11, 2013.

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.