Merseyside Fire and Rescue Service were called to Westminster United Reformed Church at 6.04 am to tackle the blaze.
In a statement it said: "Crews arrived to find an area 30 x 20 metres well alight and began firefighting to the exterior of the building with 2 main branch hoses and a high pressure hose reel.
"The area has been divided into sectors and firefighting is taking place at the front and rear of the building."
A number of roads were closed due to the severity of the fire, while locals said they could see and smell smoke.
The reason for the fire is unknown.
According to the Liverpool Echo, the church is used by rough sleepers but none were found inside.