The fire is believed to have started on the outside wall, before spreading inside the building and up to the roof, causing “severe damage”.
The building is used as a changing facility by hundreds of young footballers aged between 12 and 19, who play in the Edinburgh City youth league in the adjacent Sighthill Public Park.
Fire crews from Sighthill and Tollcross were called out to the building on Broomhouse Road at around 3am today, and were at the scene until after 5am.
The blaze is being treated as “suspicious” and an investigation is now under way.
A spokesperson for Lothian and Borders Fire and Rescue said: “It is suspected the fire was started maliciously, and an investigation is under way.”
The pavilion has been plagued by vandalism and this is the third suspected arson attack in five years.
In 2006 a fire destroyed the roof, which put the building out of use for two months.
And in April 2008 two changing rooms were completely burnt out and three other rooms were smoke-damaged.
Councillor Deidre Brock, Culture and Leisure Convenor at City of Edinburgh Council, said: “Police are still carrying out investigations but whatever the cause of this fire, it has destroyed a very well used facility. The Council and Edinburgh Leisure will now have to find alternative changing facilities for the numerous teams who rely on them for matches at Sighthill Park.”