The blaze broke out on Monday evening around the same time as Paris's Notre-Dame cathedral burned.
The fire was "quickly extinguished", Israeli police said, adding the cause was being investigated.
The Waqf religious organisation which oversees the site said the fire burned a guard's room above what is known as the Marwani prayer room.
It said the fire was caused by youths playing with fire, without providing further details.
It is considered the third-holiest site in Islam and the holiest in Judaism.
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