The incident happened just before 2:30 p.m. at Littlefield Avenue and Hylan Boulevard.
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NYPD officials say a person on the bus witnessed an argument unfold between two male teens, a 13-year-old victim and his 14-year-old attacker, who went to the same middle school.
They say a knife was taken out and gang signs were exchanged between the victim and suspect. The victim was then stabbed in the chest.
That victim has been identified as 13-year-old Syles Ular.
The 14-year-old was arrested and charged with murder, manslaughter, and weapon possession.
People on the bus who saw the attack say the mortally-wounded victim was stabbed as many as five times.
Police said the victim made it to the front of the bus and collapsed in front of the bus operator.
MTA officials said the bus driver was "amazing," and contacted the control center immediately, who requested police.
Sources say first responding officers chose not to wait for an ambulance, and instead put the victim in a cruise and rushed him to the nearest hospital. He was later pronounced dead.
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"My heart just sank into my stomach," witness Anthony Esenplare said. "I'm heartbroken for his family."
The teen suspect fled from the bus and ran about three blocks.
Officials say a good Samaritan, a retired NYPD sergeant and a New York Department of Environmental Conservation officer helped in the pursuit and capture of the suspect.
The teen was taken into custody and is being questioned. Police believe the incident may be gang-related.
"This is just a tragic, tragic day. A 13-year-old child's life lost," said Demetrius Crichlow, Senior Vice President NYC Transit Department of Subways. "It's a senseless death."
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Crichlow said the MTA is supporting the NYPD in the investigation. He said there were cameras on the bus, and that they have a "good account" of what transpired.
New York City Schools Chancellor David Banks said the incident, involving the two middle schools students, is "concerning."
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