The Unison union said its members wanted additional payments for undertaking tasks which were dirty, unpleasant, involved regularly working outside or heavy lifting.
The staff involved in the action are employed by Cordia - an arms-length body of Glasgow City Council.
All schools were open on Monday but some breakfast clubs were cancelled.
The dispute centres on a claim by janitors for a Working Context and Demands Payment, which can range from Â£500 to Â£1,000 annually.
The union has accused Cordia of "using spurious arguments to justify not making this payment" to its members.
Unison Glasgow branch officer Sam Macartney said: "Unison is very clear that school janitors meet the criteria to be awarded this payment.
"Our members have been left with no option other than to take this action as both Cordia and the council are wrong and just not listening to our members.
"The council needs to get round the table with Unison and agree a negotiated settlement of our members' legitimate claim."
Janitors on strike turned up at the City Chambers on Monday "with buckets, mops and brooms" to stage a demonstration. Another will be held on Tuesday.
Picket lines were organised on Monday morning with a repeat planned for Wednesday.
The union said teachers, support workers, cleaners and catering staff had been advised by their unions not to undertake the duties of janitors in their absence.
A council spokesman said: "Some of the city's janitors took part in industrial action in a number of our primary, Additional Support for Learning schools and nurseries today, with similar action planned for Tuesday and Wednesday of this week.
"This action unfortunately meant that Breakfast Clubs in affected schools had to be cancelled."
More than 100 school janitors in Glasgow have begun a three-day strike in a dispute over pay.