The money is returned to customers when trains are more than 15 minutes late. Metrolinx, the transit authority that governs Go, has a Guaranteed Service clause which allows people to ride for free if the delay is caused by something Go can control.
The transit agency blames February's frigid temperatures for the late trains.
"Sometimes the door freezes, so they can't shut properly and you can't move a train if they are not shutting properly," said Metrolinx spokeperson Anne Marie Aikins.
The fare rebate is available online for those who use Presto Cards.
"You fill in the blanks with your trip number and date the card number and then its reimbursed to your card if that trip qualifies," said Aikins.
Guaranteed Service on Go trains has been offered for just over two years. Metrolinx says the rebates are popular but it didn't have the exact figures on how many riders qualify get their money back.