The incident happened Thursday after 5 p.m. as the ferry was headed from Lower Manhattan to Staten Island.
The fire started inside the engine room. Crews onboard put CO2 into the engine which helped subdue the fire.
WATCH | Passenger describes evacuation from Staten Island Ferry
Passenger describes evacuation from Staten Island Ferry
Upon arrival, the FDNY's main goal was to secure the vessel and get passengers offloaded onto other boats.
The ferry was temporarily anchored, allowing passengers to be removed safely onto separate tugboats.
The ferry was able to make it to Staten Island and all the passengers were brought to the St. George Ferry Terminal.
FDNY officials said 868 passengers and 16 crew members were onboard at the time.
They said five people suffered minor injuries. Three of those victims were taken to an area hospital.
The FDNY will now monitor the temperatures in the engine room for the next 24 hours to determine when it's safe to enter.