The ballot saw a turnout of 68% (37,000), with 42% voting in favour of accepting the contract and 58% voting to reject it.
In May, BMA officials and the government finally agreed on new terms for junior NHS doctors in England, after a long and bitter dispute.
The BMA however insisted on putting the deal to a vote of its membership of junior doctors and medical students in the final two years of their training.
A series of 130 road shows was conducted across England to ensure that doctors fully understood the implications of the new contract.
Immediately after the result was known, Dr Johann Malawana, chair of the BMA’s junior doctor committee, resigned. Malawana had led the negotiations on behalf of the BMA in the dispute.
Commenting on the result, Malawana called on the government to “respect the informed decision junior doctors have made”. He said any “new contract will affect a generation of doctors working for the NHS in England, so it is vital it has the confidence of the profession”.
Malawana added that both sides “must look again at the proposals” but said there should be no transition to a new contract until further talks take place.
The government had been keen to push ahead with the agreement, which would have seen new rotas for 6,000 newly qualified doctors brought in by August. Many of the remaining 55,000 junior doctors would move to the new arrangement from that point onwards.
Under the deal, the pay rise offered to junior doctors had been reduced, along with night shift pay, and the distinction between ‘normal’ and ‘unsocial' hours removed.
As to why the membership rejected the deal, Malawana said: “Having spoken to many junior doctors across the country in recent weeks it was clear that, while some felt the new contract represented an improved offer, others had reservations about what it meant for their working lives, their patients and the future delivery of care in the NHS.”
He added that there was “considerable anger and mistrust towards the government’s handling of this dispute” and warned that a “fundamental breakdown in trust caused by the government’s actions over the last five years has resulted in a situation where no solution is possible”.
Responding to the ballot, health secretary Jeremy Hunt said the result was “extremely disappointing”.
He added: “The BMA’s figures show that only 40% of those eligible actually voted against this contract, and a third of BMA members didn’t vote at all. We will now consider the outcome.”
Danny Mortimer, chief executive of NHS Employers, was one of the main negotiators in talks. He said: “I am profoundly disappointed the BMA has rejected the proposed new contract for junior doctors. It is imperative that patients will not be made to suffer any further impact as a result of the rejection of the contract.”