It happened around 2:00 Saturday morning on the 4600 block of Worth Street.
Authorities say the officer, from the 15th district, came across a man armed with a gun who was running down the street.
A chase ensued and the man allegedly pointed a gun at the officer.
The officer opened fire, striking the man in the head. He was pronounced dead at the scene.
No word why the suspect was running and his identity has not yet been released.
The Philadelphia officer who fired the fatal shot will be placed on desk duty as the incident remains under investigation.