The armed suspects attacked the Santa Maria Church in the Sariyer district at 11:40am local time.
Footage obtained by Reuters shows the attackers enter and leave the church.
Interior Minister Ali Yerlikaya condemned the attack during Sunday service and said authorities are working on capturing the assailants.
The victim who was killed while attending the service was a Turkish national. Officials said the attackers only fired at one person.
No other injuries have been reported.
It remains unclear what the motive for the attack was or why the victim was targeted.