Police said the motorcyclist, identified as Mauricio Galdamez of Jamaica, was driving east on Union Turnpike around 1 a.m. and sped through a red light at the intersection of Springfield Boulevard.
Galdamez crashed his motorcycle into the bus as it passed through the intersection, police said.
He hit the bus near the driver's side window and was later pronounced dead at the hospital.
The intersection was closed for a time while authorities investigated.
The MTA said the number or route of the bus involved in the accident wasn't immediately available.