Police with sniffer dogs boarded the A319 passenger plane after being called to security concerns at 7.40pm on Wednesday.
The runway had to be closed for 50 minutes as the aircraft was moved to a “secure area” while scores of other jets circled above waiting to land.
Specialist officers boarded and searched the aircraft before declaring it safe.
Essex Police said they arrested three men on suspicion of making a bomb hoax. They remain in custody.
A spokesman for Essex Police said: “Following a search of the plane we are satisfied there is nothing of concern on board.
“We want to thank the other passengers on board for their patience and understanding.”
The airport has now fully reopened, a spokesman for Stansted Airport said.
An earlier statement said: “A flight due to depart from Stansted to Amsterdam is currently parked on a remote stand while police conduct extra security checks.
“The airport’s runway was closed for a short time but has now fully re-opened.”
