This was after Safaricom ordered the firm to effect the refunds after some 424,011 requests never returned results.
Candidates, guardians and schools were asked to send index numbers to short code 22252 to receive their results at Sh25 per SMS.
This means Challa will have to part with at least Sh10.6 million.
"Dear customer, we apologise for your recent inconvenience using the KCPE short-code. We have refunded Sh50 for deductions done without service delivery," an SMS from Challa to a customer read.
The refunds are for customers whose queries never received a response and those who sent requests more than once due to delays.
Safaricom director of strategy Joe Ogutu said in a statement on November 23 that Challa had informed them the problem was caused by a technical hitch on its systems.