Councillors voted against debating the proposals to increase capacity by eight million to 43 million passengers a year.
Uttlesford District Council voted by ten votes to 2 abstentions to overturn a previous decision to allow the airport to go ahead with the plans.
The plans were first approved 14 months ago but were never rubber stamped.
And the council said it was growing concerns over climate change which meant they had taken the decision.
Speaking to our reporter Claire McGalsson, Councillor Colin Day said the council had a duty of care toward residents.
Stansted are considering whether to appeal, but this evening issued a statement:
It was two years ago that Stansted Airport first made an application, but it was never confirmed.
The boss of Stansted Airport has written to local residents, saying that growth would be “in the best interests of the community”. The CEO Ken O'Toole has also written an open letter to local residents, setting out the airport’s future plans, arguing that they will benefit the region.
However, growing concern about climate change means campaigners now believe they can stop the expansion in its tracks.
- Check out Claire McGlasson's report for more. Claire looks at how the issue has developed over the past two years, and talks through some of the key points from the meeting so far.