Essex Police said the two men arrested on suspicion of endangerment of an aircraft are both British nationals.
The men, aged 30 and 41, are currently at a police station where they will be interviewed by detectives.
Essex Police said the plane that was diverted to Stansted Airport will remain at its current location until it is examined by forensic experts.
"At this point in time no suspicious items have been recovered", Superintendent Darrin Tomkins said.
"This incident is being treated as a criminal offence and remains under the direction of Essex Police", he added.
More top news
The man identified as the Islamic State militant known as "Jihadi John" was a "popular" schoolboy who loved Manchester Utd and S Club 7.
Everton, the only British side left in the Europa League, have been handed a tough tie against Dynamo Kyiv in the last 16 round
Ukip remains the party most trusted to control immigration despite more people seeing them as racist, a ComRes/ITV News poll has found.