British Medical Association (BMA) union members voted 58 per cent to 42 per cent against accepting the deal, despite the BMA having urged them to accept the terms.
The new terms had been announced in May after talks with the government resumed following six strikes since late 2015.
Dr Johann Malawana, chair of the BMA junior doctors' committee, announced his resignation after the ballot result was released today.
"There was also considerable anger and mistrust towards the government's handling of this dispute. These concerns need to be fully addressed before any new contract can come into effect.
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"There is much to do to in order to rebuild the trust that has been eroded over the last year. The government must now do the right thing, accept the outcome of this vote and work constructively with the BMA to address junior doctors' concerns with the new contract."
"We will now consider the outcome," he said after today's vote.
In May, it was announced that talks at conciliation service ACAS had finally resulted in a deal being agreed to end the long-running dispute between the doctors and the health ministry, but the union had said it would put the terms and conditions to a vote of members.
More than 100 road shows were organised where union leaders met with members to explain the new deal, which differed substantially from what the government had previously offered.
But many members remained unconvinced, believing it still did not properly reward them for the demands of the job.
The vote was open to 54,000 BMA members - junior doctors and medical students in their final two years of their degree - and now raises the prospect of further strike action unless another deal can be struck.