Phipps, 19, was signed by the Stones in December 2016 from Margate.
The midfielder had attracted interest from several clubs after his stand-out performances for the Kent club.
He made his Gate debut from the substitutes bench in a game against Sutton United in February 2016 and featured consistently for them after that.
Phipps was previously at Gillingham’s academy in Canterbury and also played for the Stones under-15s a few years ago.
He had two separate loan spells with National League South side Welling United this season, only returning from his second on New Year`s Day.