They will play in the Under 21 East Division next season, with home matches played on Saturday mornings at Sign Right Park.
The division will include AFC Rushden & Diamonds, Barwell, Coalville Town, Nuneaton Borough, Quorn, FCV Stamford, Leamington, LFE Academy, Loughborough University and Rugby Borough.
The newly-formed Melton team will move to the club from Stoneygate Lions with Vincent John continuing as their coach.
“I’ve actually had most of the team together since they were under 12s at Syston,” he told Town’s website.
“We had played at AFC Andrews for a spell, but when they decided not to enter an under 18 side we moved over to Stoneygate. I want to keep this squad of players together and help them to push on in to first team football.”