
The early morning action by some 50 protestors from the group Plane Stupid had closed the airport's single runway, paralyzing all traffic.
A total of 21 flights were cancelled, as long queues formed at check-in desks and many passengers chose to return home or seek hotel accommodation, reports said.
Up to 40 protestors of the group, which managed to break through a tall security fence at around 0300 GMT Monday, were arrested, police said.
Stansted, some 50 kilometres north-east of London, is the British capital's third-biggest airport predominantly used by budget airlines, including Ryanair, for European routes.
Airport operator BAA earlier warned of severe delays and advised passengers to check with airlines before setting out.
Plane Stupid said the protest was to highlight the "hypocrisy" between government climate change goals and reality.
"We're here because our parents' generation has failed us and its now down to young people to stop climate change by whatever peaceful means we have left," a statement posted on the group's website said.
"Being arrested is a terrifying prospect, but not nearly as terrifying as the threat of climate change," one female protestor told the BBC Monday.
The protest is over the government's decision to allow the expansion of Stansted with a second runway, a plan that has met widespread opposition from residents in nearby towns and villages.//dpa