Those starting out in the medical field, the Scottish Government said, will see an increase of £3,418, rising to £7,088 by the end of their training.
According to BMA Scotland, 98.2% of respondents backed the offer, with a turnout of 61.4%.
Health Secretary Neil Gray said: “I am very pleased that resident doctors and dentists in training have voted to accept the Scottish Government’s pay offer.
“This demonstrates how much we value them and ensures that NHS Scotland remains the place of choice to work and train.
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“I am pleased we have been able to work together to honour the previous agreement from 2023-24 and I extend my sincere thanks to our hard-working resident doctors and dentists in training.”
Dr Chris Smith, chairman of BMA Scotland’s resident doctor committee, welcomed the acceptance, but warned against Scottish Government complacency.
He said: “Today is another important step forward for Scottish resident doctors, but there is still significant work to be done to achieve full pay restoration, which is a vital step towards keeping the doctors we need in Scotland for the benefit of the NHS and ultimately patients.
“This result sends two clear messages to the Scottish Government.
“Firstly, that doctors are united behind their union and the campaign for full pay restoration. Secondly, it shows that the framework deal agreed in 23-24 – and built on with this accepted deal for 24-25 – is essential to moving forwards constructively.
“The Scottish Government must continue to build on the agreements that we have reached so that doctors have confidence that our current trajectory towards full pay restoration – and the true recognition of our skills, sacrifices, and responsibility – is satisfactory and sustainable.
“We are still only around halfway towards rectifying the historic pay erosion inflicted on Scottish resident doctors.
“We have had two years of solid progress, but if the Scottish Government were to slow down or become complacent now, it would be extremely damaging for relations with the medical profession and therefore for what the health service is able to deliver for patients.
“To be clear, while we have so far seen negotiations conducted robustly, but in good faith, any signs that progress is starting to slow or stop in coming years will be met with a resolute and united profession clear in its view that the deal done simply must be delivered in full.”