Queensland's south-east rail network will return to full service by the end of November, after the state government and unions settled a long-running pay dispute.

Queensland Rail (QR) and seven unions have been negotiating in the Fair Work Commission since May, with protected industrial action and a maintenance backlog resulting in reduced services and frequent delays for commuters.

Transport minister Brent Mickelberg said an in-principal agreement had been reached, with trains to return to a normal timetable in a staged rollout from next month.

"We can restore 91 per cent of services from the 12th of October, and we will aim to restore all services by the end of November," he said.

"I do want to emphasise that I acknowledge the impost this has placed on commuters over an extended period of time, and it's been a challenging process negotiating with a number of unions across seven different agreements."

QR head of corporate affairs, Nev Conway, said the operator would now work as quickly as possible to clear the maintenance backlog.

"There'll be a reinstatement of 417 services each week, or about 83 extra trains a day," he said.

"Customers will notice a significant improvement in the frequency and the comfort on board once we get to that 91 per cent, and then we'll work through the rest of the rolling stock and get back to a full timetable in November."

Impacted QR employees will now vote on the enterprise agreement, which offers an 8.5 per cent pay rise over three years, and a further uplift dependent on inflation.

Rail, Tram and Bus Union (RTBU) branch secretary Peter Allen said real improvements to conditions had been secured.

"This outcome was achieved not because of Queensland Rail and the Queensland government, but almost in spite of them, after months of games and delay at the bargaining table," Mr Allen said.

"With an agreement now in place, QR and the Queensland government have run out of excuses — it's time they got full services running for the travelling public."

Mr Mickelberg did not reveal the full cost of the new agreement but said it was in line with the government wages policy.

"We held a relatively hard line, and we deliberately drove a deal that was reflective of both taxpayers' money and reflective of the workforce that delivers an important capability for Queenslanders," he said.

"We'll continue to take that approach in enterprise bargaining arrangements."

QR signed off on a deal for around half of its almost 6,000-strong workforce in June, and last month reached an agreement with the union representing almost 300 train controllers.

The Electrical Trades Union (ETU), Australian Manufacturing Workers' Union (AMWU), and The Services Union (TSU) have been contacted for comment.