Kathon Anderson is charged with second-degree murder.
Authorities say the suspect boarded the bus to go after a rival gang member, but instead hit 39-year old Angel Rojas in the head.
The teenager was arrested at the scene while commuters scrambled to get out of the way. A firearm was recovered.
Police said the boy fired one shot on the bus and several more outside. Six shell casings were found at the scene. The shooting appears to be gang related, and authorites say the intended target was a member of a rival gang who had been taunting him on social media.
Girls he was with reportedly pointed out the target.
The boy has a prior arrest for an assault as a hate crime in 2011, authorities say. He was charged as a minor, and the arrest is sealed.