Direct Debit payments for the Kent Travel Saver Card and its 16+ equivalent will be cancelled in January and February due to the national lockdown.
Vulnerable children and those of critical workers will still be able to use their pass to travel to school.
A refund for those that have paid upfront will be made once a decision is made by Government on when all children may return to school.
KCC Cabinet Member for Highways and Transport Michael Payne said: “We appreciate how hard another lockdown is for parents and the impact it is having on families, businesses and livelihoods, particularly after it follows some of the harshest tier restrictions.
“This situation has created another very complex problem and KCC officers have been working behind the scenes on the best way to help those that purchased a Kent Travel Saver but are now not currently able to use it because of the lockdown restrictions.
“Although the Kent Travel Saver cards are normally non-refundable, KCC believes it is only right not to collect the January and February Direct Debit payments.
“Furthermore, we will make a decision about the March payment when we are hopefully better informed about the timetable for the return to school.
“We will also review the level of refund for those who have paid upfront in full once we know the timescale for all pupils to be allowed to return.”
The KCC Travel Saver and KCC 16+ Travel Saver are subsidised by the council and can save up to 50% on the cost of travel to and from school.
County Councillor Barry Lewis said: “I am delighted they have eventually seen sense and bowed to public pressure. Hopefully this will ease the financial pressures on Thanet families.”