A crossfield ball found Emilio Lawrence in space, he flashed a cross across the six-yard box for Harrison who was there to apply the finish.
City were stung just after the half an hour mark as the visitors scored two goals in a minute to turn the game on its head.
Defender Jake Griffin pulled the scores level, heading home from a corner before captain Nathan Lowe fired in a rebound after George Murray-Jones’ initial save.
Lowe scored his second and Stoke’s third of the game in the second half - making City’s task of progressing through to the quarter finals even more difficult.
Michael Okeke rattled a post later on in the game, but we could not find a way back into it.
The defeat to the Potters sends us out of the Under-17s Premier League Cup.
Click on the above video to see the best of the action...