Private schools have been barred from increasing their fees by more than five percent a year.
On Monday, the Sindh High Court ruled that it is illegal.
Private schools are already prohibited from doing this under the existing regulations.
The Parents Action Committee, which includes more than 100 people, had gone to court against four private schools that keep breaking the rules; Head Start School, Beaconhouse School, The City School and Foundation Public School.
The schools have been ordered to return or adjust the extra amount they charged parents within the next three months.
The schools argued that they increased the fees according to the law.
They added that their legal and maintenance costs are too high.
They explained that their main costs include an increase in salaries for teachers, electricity bills and campus security.
The judges had made their decision on June 6 and announced it today (Monday).
On March 6, justices Munib Akhtar and Arshan Hussain Khan had restricted the schools from increasing the tuition fee beyond the 5% allowed under the law.
The Sindh education department was told to submit quarterly reports on private school audits, and the enforcement of its orders.