A spokeswoman for Ulster Bank said fewer than 500 customers were hit by the overcharging. The Central Bank has been informed and full refunds and back payments of interest would be sent to customers, she added.
Most of the customers affected are understood to have originally taken out tracker mortgages with [broken link removed], which has since been absorbed into Ulster Bank.
The spokeswoman said: "Ulster Bank can confirm that following an internal review, a number of mortgage accounts have been identified whereby an incorrect tracker margin has been applied.
"They will receive a full refund of any overpayment plus compound interest owed and the correct tracker margin will be applied for future repayments."