Two goals in the final quarter of the match proved the difference in the first round of a competition that the Yellows won three seasons ago.
Manager Paul Carden selected just two players that started Saturday’s league win over Mickleover Sports – goalkeeper Luke Pilling and centre-half Jack Higgins – while Steve Jennings made his second debut for the club having completed a permanent move from Southport.
Four youngsters were drafted in from the Robbie Fowler Football Academy, alongside Jamie Davis, who had already featured in the Yellows first team.
It was largely a game to forget for the 108 in attendance, the two sides restricted to a couple of edge the box efforts from Stephen Milne for the hosts and Charlie Bailey for Lancaster.
One of the youngsters, Gilson Amaral, was well placed to stop Mamadou Djabi’s shot on the line 10 minutes in to the second half, and Djabi also forced a good stop out of Pilling.
The deadlock was broken on 67 minutes by a former Warrington player, Ryan Winder, who converted from the penalty spot after Bailey was hauled down by Higgins.
Lancaster looked the more likely and they put themselves in a commanding position 15 minutes from time when Richard Mercer rose unmarked to head home Winder’s corner for 2-0.
Warrington Town must now prepare for a daunting three games in four days – trips to Hednesford (Saturday) and Grantham (Tuesday) in the league sandwich are Cheshire Senior Cup game at home to Winsford (Monday).
Warrington Town: Pilling, Amaral, Cunningham, Jennings (Williams), Higgins, Banks, Shield (Kinsella), Bakare, Piggott, Milne (McDonald), Davis. Unused subs: McMillan, Carden.
Lancaster City: Wynne, Steele, Sumner, Wills, Anson, Mercer, Creech (Jarvis), Carney (Tam), Djabi, Bailey, Winder. Unused subs: Bailey, Dugdale, Williams.