A spokesman for the airport, in Essex, said police were on the scene after the passenger plane was diverted from its route between Kaunas, Lithuania, and Luton Airport, in Bedfordshire.
He added all flights had now resumed after being held for about ten minutes from 8.55am on Wednesday.
“Flights were briefly held while RAF Typhoons escorted the plane in.
“All flights are now operating as normal;. It was literally a momentary pause.”
Essex Police tweeted: “We are aware of an incident at Stansted Airport. We will bring you more information when we can.”
A Ryanair spokesman said: “This flight from Kaunas to London Luton diverted to London Stansted in line with procedures after Lithuanian authorities received a suspected hoax security alert.
“The aircraft landed normally at Stansted and customers will be transferred to Luton by coach when cleared to do so.”
The jets were sent from RAF Coningsby, Lincolnshire to intercept the flight, the Ministry of Defence said.
A sonic boom echoed across the Suffolk skyline when the jets were scrambled, Suffolk Police confirmed.
An RAF spokesman said: “The RAF can confirm Quick Reaction Alert Typhoon aircraft were launched this morning from RAF Coningsby to intercept a civilian aircraft.
“The aircraft was safely escorted to Stansted Airport. The Typhoon aircraft were authorised to transit at supersonic speed for operational reasons; any inconvenience caused to local residents is regretted.”