Coming just two days after a long trip to Hartlepool and with four Under 16s in the line up it was another tough test against Dave Bentley's youngsters who always try and play good football.
But an early penalty from Thomas set the young Imps on their way and despite the hosts drawing level before half-time, it was City who got stronger as the game went on.
Rob Smith enjoyed his finest game yet and was a constant threat breaking from midfield, while Eddie Jones, Matt Cotton and skipper Thomas all came close to finding the winner.
The Youths now take a well earned break from league football and can be very proud of how they have represented the Football Club this season.
Team: Smith H, Bowkett, Walker, Cotton, Ward, Griffin, Thomas, Bowles, Helsdown, Smith R, Simmons. Subs: Cooke, Jones, Harper, Barr-Rostron.