The schools, both in the East End, were broken into on Saturday afternoon and wrecked.
Parkhill Secondary School, for children with learning difficulties, in Cumbernauld Road, had two windows smashed, and the ground-floor classrooms, offices and the kitchen ransacked.
It was broken into at around 2.30pm.
Meanwhile, St Timothy's Primary School, in Inveresk Street, was broken into at around 3.30pm. Almost the entire school was ransacked including the nursery area.
In both cases, a council spokesman said nothing appeared to have been stolen. He described the break-ins as "sickening".
Schools across the city closed down for the festive holidays on Friday and are to return after the New Year.
The damage at Park-hill and St Timothy's will be repaired by the time the pupils are due to get back.
A council spokesman said: "Although nothing appears to have been stolen, both schools were ransacked. For this to have happened just after the pupils and staff left for the Christmas holidays is sickening and we would urge anyone who has any information to contact the police.
"We will clear the mess and repair the damage in time for pupils returning after New Year."
Last week, two iPads and £600 was stolen from Quarrybrae Primary, in Shettleston, during a break in on December 17.