Plans to build the second phase of the Oxford to Cambridge East-West rail scheme have been submitted by Network Rail to the Secretary of State for Transport.
If approved it could mean, for the first time in 50 years, trains would run again between Oxford and Bedford and Milton Keynes and Aylesbury.
It has been hailed as a "significant milestone" by rail campaigners.
With consent, track and signalling upgrades could start in 2019.
A "mothballed" section of the track, between Bletchley and Claydon Junction, would be "brought back to life", said Network Rail.
The proposed routes are:
- Oxford to Milton Keynes, with trains stopping at Oxford Parkway, Bicester, Winslow and Bletchley
- Oxford to Bedford, with trains stopping at Oxford Parkway, Bicester, Winslow, Bletchley, Woburn Sands and Ridgmont
- Milton Keynes to Aylesbury, with trains stopping at Bletchley, Winslow and Aylesbury Vale Parkway
Colin Murphy, from Network Rail, said: "Once completed, the new railway will connect communities and businesses along the route and beyond, creating new opportunities for jobs, housing and economic growth."
The East West Railway Company will oversee the delivery of the project, which aims to reconnect the university cities of Oxford and Cambridge by rail, half a century after the "Varsity Line" was closed.
Mark Shaw, chairman of the East West Rail consortium of local councils, said: "After more than 20 years of campaigning, the submission is a hugely significant milestone."
Phase One of the scheme, which connects Oxford and Bicester was completed in December 2016.
The third phase, reconnecting Bedford to Cambridge, is currently in development.
Dave Hodgson, Elected Mayor of Bedford and chairman of England's Economic Heartland's Strategic Transport Forum, said: "We now need the route between Bedford and Cambridge to be confirmed as soon as possible, so that delivery of the full scheme can be achieved within the government's stated target of the mid-2020s."