The latest issue to beset a bank already plagued by computer failures saw some ATM users debited twice for single withdrawals.
The problem lasted for a 24 hour period during Monday and Tuesday of this week.
Ulster Bank has suffered from a range of IT failings over the last two years - a number of which have been linked to its parent company RBS.
The worst came in the summer of 2012 when some Ulster Bank customers were left with limited access to their accounts for three weeks
It is understood only Northern Ireland customers of the all-island lender were impacted by the most recent problem.
A spokesman for Ulster Bank said it hoped money would be refunded into accounts by tonight.
"We are aware of an issue regarding duplicate ATM transactions involving some Ulster Bank customers between 4.15pm on Easter Monday and 4.15pm Tuesday afternoon," he said.
"We are working to correct this for affected customers and restore money to accounts tonight.
"Customers will not be left out of pocket as a result and can contact us if they require further assistance.
"We apologise for any inconvenience caused."