The Rail, Maritime and Transport union (RMT) said the deal includes “significant uplifts” in salaries, including backpay which it added goes some way to address the “suppression” of pay over many years.
Shorter assignments and better work-life balance arrangements are also included, said the union, which held a number of strikes last year over the row.
RMT general secretary Mick Lynch said: “This is a fantastic result for our RFA members, who’ve stood strong, united and taken several bouts of strike action during this dispute.
“They’ve secured real-terms pay increases, important improvements to their working lives and I thank them for their efforts.
“This agreement lays the groundwork for securing their future and vital role assisting the Royal Navy.
“RMT will keep fighting to ensure the contributions of RFA workers are properly recognised going forward.
“We now go in to a phase of serious discussions with the RFA and MoD on the future structure of the RFA, their conditions of service and salaries in which we expect to make further significant improvements for our members.”