"Our systems are fully operational and air traffic capacity is returning to normal," NATS, the country's air traffic control provider, said in a post on X.
"Departures at all airports have resumed and we are working with affected airlines and airports to clear the backlog safely. We apologise to everyone affected by this issue."
The outage, announced by NATS 20 minutes earlier, included Heathrow Airport, the UK's largest and Europe's busiest.
"Flights at Heathrow have resumed following a technical issue at the NATS Swanwick air traffic control centre. We are advising passengers to check with their airline before travelling," an airport spokesperson said.
Gatwick Airport and Edinburgh Airport also said operations were resuming.
London City Airport had earlier also reported disruption.
It was not clear exactly how long the outage had lasted.
Ryanair said the disruption lasted for "over four hours" and caused delays and several diversions, inconveniencing thousands of passengers.
The Irish low-budget airline said the problem was "utterly unacceptable" and called for Martin Rolfe, the chief executive of the air traffic control provider, to resign.
"It is clear that no lessons have been learnt since the Aug '23 NATS system outage and passengers continue to suffer as a result of Martin Rolfe's incompetence," Ryanair chief operating officer Neal McMahon said in a statement.
In August 2023, flights across the UK were disrupted after the automatic processing of flight plans malfunctioned.
Last year, the UK aviation regulator said NATS needed to review its contingency plans for outages after the disruption, which airline bosses said cost them more than 100 million pounds ($A206 million) in refunds and compensation.
