Crews were called to St Paul's on Muirhouse Avenue at around 9:15 on Sunday night.
Around 20 firefighters had to battle the blaze. No-one was injured.
The Catholic Church hasn't been in use since October and is up for sale for development.
A Police Scotland spokesman said: "Police in Edinburgh responded along with the Scottish Fire and Rescue Service to the vacant St Paul's church on Muirhouse Avenue at around 9.15pm following reports of a fire.
"The fire is being treated as suspicious and anyone with any information is asked to come forward."
