A number of customers contacted Nationwide's customer services via social media to complain about the problem.
The problem, thought to have been connected to maintenance work, was fixed after about 45 minutes.
Nationwide has apologised for the inconvenience.
Cash machines were unaffected by the problem.
Many banks and building societies have suffered from temporary faults on their online banking services, but they rarely last more than a few hours.
The fault comes the day after the Bank of England suffered a technical problem with the technology underpinning a same-day, high-value payment system.
The UK's largest building society - the Nationwide - suffered a technical problem with its online and mobile banking service during the afternoon.