Previous talks collapsed in December 2023 after the BMA rejected a proposal it said was worth an average of an extra 3% on top of 8.8% already received.
Junior doctors are seeking a pay rise of 35% in compensation for below inflation rises since 2008.
There have been 10 walkouts by workers since the beginning of industrial action in March 2023.
Senior doctors in England agreed to end their industrial action in April 2024 after accepting a rise of up to 20% in 2023-24.
Industrial action by consultants and specialist doctors in Wales was also called off in April 2024 following a "significant proposal" from the government.
Junior doctors in Northern Ireland are planning two 48 hour strikes on 22 May and 6 June.
Junior doctors committee co-chairs Dr Robert Laurenson and Dr Vivek Trivedi said: 'We have been in dispute for more than a year with the Government over declining junior doctor pay, exploring various avenues to try and resolve it.
'We have been looking at ways of restoring trust between parties and believe that an independent mediator can help break the logjam.
'We hope to reach a credible solution as soon as possible.'
Health and social care secretary, Victoria Atkins, said: 'As secretary of state for health and social care, my duty is to patients and I want to pursue all avenues to resolve the dispute with the BMA junior doctors committee.
'This will ensure they can focus on delivering the highest quality care and help consolidate our recent progress on waiting lists.
'I am pleased the BMA have agreed to explore mediation and I am hopeful that it will provide a way forward.'
Deputy chief executive of NHS Providers, Saffron Cordery said: 'Today's announcement takes us another step closer to resolving pay disputes and strike action which has caused major disruption to patient care and NHS services over the past 18 months.
'While trust leaders know this isn't a done deal, the decision by the BMA's SAS leadership to recommend doctors vote to accept this offer in the coming weeks is a step forward.
'Trust leaders will also be cautiously optimistic about progress in talks between junior doctors and the government, who have now agreed to explore mediation in their longstanding dispute.
'With the NHS under sustained pressure, it's vital we do everything possible to draw a line under industrial action across the health service while working together to improve conditions for our highly-valued staff.'
