More than 200 planes were delayed at the London airport after a thunderstorm and lightning strikes overnight.
Another 31 departures and 18 arrivals were also cancelled on Sunday morning at the airport on the Essex-Hertfordshire border, according to FlightStats.
Disruption and delays continued after the damage was repaired and passengers were warned to check before travelling.
Customers complained on social media about queues at security and delays on the tarmac.
Chiara Elisei tweeted: “Stuck on a plane in #Stansted with #nofuel and no idea of when and if we will be departing. Ridiculous. A country in freefall.”
John Mann MP posted that “nothing” was leaving the airport and there were “empty skies”.
Stansted said in a statement: “Due to an earlier lightning strike, the aircraft fuelling system was unavailable for a period this morning.
“Engineers have been on site and have now restored the system, however flights may still be subject to diversion, delay or cancellation.
“We apologise for the inconvenience and advise all passengers to check with their airlines for their latest flight updates.”
Ryanair could not say how many of its flights had been affected, and said customers can get a full refund or free transfer.
“A number of flights have regrettably been cancelled at Stansted Airport this morning due to an earlier airport fuelling system failure, caused by a lightning strike,” a spokesman said.
“All affected customers are being contacted and advised of their options of a full refund, a free transfer on to the next available flight or a free transfer on to an alternative routing.
“We apologise to all customers affected by these disruptions, which are entirely beyond our control.”