A total of 29, 500 flights were expected across the continent with almost half of them being slowed by the outage in the Enhanced Tactical Flow Management System at the Eurocontrol centre in Brussels.
Doncaster Sheffield Airport has not yet commented on whether or not their flights have been affected.
There were no major delays showing on the airport's website this evening.
The fault, which risked disrupting the travel plans of up to half a million passengers, has now been identified.
Eurocontrol, which coordinates air traffic across 41 countries, said it expected the system to be back up and running later this evening.
They added the breakdown hit the system for flight management but did not hit traffic control or security.