The strike ballot will be open from Friday until 19 December. In the event of a yes vote, industrial action is likely to take place in the first few weeks of the new year.
The ballot opens as resident doctors in England begin a five-day walkout.
Dr Chris Smith, chairman of the BMA's Scottish resident doctor committee, said: "Doctors have been shocked that the Scottish government seem to be intent on throwing away the progress made in restoring our pay over the last two years and are clear they will stand up to protect the deal which was agreed in good faith by both sides.
"As always, we are ready to negotiate at any time and any place. But we will not sit idle while the Scottish government attempts to break the deal that they struck with Scottish resident doctors in 2023."
He said 14 November was a "hugely significant day" for both resident doctors in Scotland and south of the border.
"I know I speak for all Scottish doctors when I say we stand beside them," he said.
"The Scottish government now has the chance to draw a dividing line between them and Westminster, and all that requires is to revert to the status quo: return to the negotiating room with BMA Scotland, in good faith and with a credible pay offer in line with the promises they made in the deal we signed."
He added: "Until now, Scotland has been the only nation in the UK to avoid industrial action and there is time to avert this action – but only if the Scottish government honours the commitment it made."