Crews were called to the Elim Rock Church in Morningside Road shortly after 7pm.
There were no reports of casualties.
The fire, which broke out in the church roof, was attended by firefighters using high pressure pumps and specialist appliances.
A spokesperson for Lothian and Borders Fire and Rescue Service said the fire was treated as a chemical incident as the church roof was found to contain asbestos.
The spokesperson added that an asbestos-clearing firm would visit the church premises today.