Previously banks made £200m a year from penalty fees on items which were unpaid because there were insufficient funds in the account.
The FCA decided this was unfair on customers because regular deductions, such as direct debits, tend to be removed first thing in the morning.
Now 7 of the biggest banks - including Barclays, HSBC and RBS -- have agreed to operate a retry system in the afternoon, probably between 3pm and 4pm, which takes accounts of new credits, salary payments and cheques which have cleared during the day.
Lloyds Banking Group has also signed up, but says as yet it's unable to retry all payments in the afternoon.
Until its systems are updated, any Lloyds customer who incurs a late payment charge because money hasn't been properly credited will be able to claim a refund.