Clifton, 18, spent the 2016-17 season on loan with Grantham Town in the Evo-Stik League Northern Premier division.
He turned professional in July 2015 after coming through the academy, but is yet to play a game for the Mariners, who finished 14th this season.
However, Clifton has earned a new deal after impressing manager Russell Slade, who replaced Marcus Bignot in April.
Midfielder Harry Clifton has signed a one-year contract extension with League Two side Grimsby Town.