The free-standing wall in the bike shed at Craiglockhart Primary School was pulled down to ensure its safety.
Edinburgh City Council has been checking scores of school buildings following the death of Keane Wallis-Bennett at Liberton High School on Tuesday.
She was crushed after a free-standing "modesty wall" fell in the school gym.
So far structural experts from the council have inspected more than 200 premises, including all primary, secondary, special and nursery schools, leisure and community centres.
Free-standing walls have been found in changing rooms and toilets at Leith Academy and Castlebrae High School, as well as in 11 primary schools.
Council chief executive Sue Bruce said: "Since Tuesday's tragic incident, we have acted swiftly to provide reassurance to parents, pupils and the people of Edinburgh that we will do everything in our power to prevent anything like this happening again.
"A member of staff at Craiglockhart Primary School made us aware of an external free-standing wall which he felt merited further inspection.
"As a result, this has now been removed."