The following is a list of MTV Pilipinas winners for Best Animated Video. The said category is one of the seven new categories added in 2006 along with Favorite Pop Video, Favorite Hip-Hop and R&B Video, Favorite Rock Video, Best Cinematography in a Video, Best Editing in a Video and Best Production Design in a Video.

Year	Artist	Video
2006	MOJOFLY MOJOFLY MOJOFLY is a now defunct pop-rock band from the Philippines.Formed in '99 by bassist Ricci Gurango after his departure from Hungry Young Poets, MOJOFLY reeled in mainstream and alternative crowds alike with the debut album Birth Day and follow-up A Million Stories , both released under Sony BMG...	Tumatakbo