Rovers made a slow start and fell behind on six minutes when Brice Wassi gave away a penalty.
Humphreys equalised with his first of the game on 22 minutes, before Jordan Preston fired Rovers in front moments later.
Humphreys grabbed his second on 28 minutes, before completely his hat-trick straight after the restart.
Antonie Boland headed home Rovers' fifth and Dean Rittenberg also got on the scoresheet, as Rovers ran out comfortable 6-2 winners.
Youth team coach Terry McPhillips said: "We were poor for the first 20 minutes, but then for the next hour we played some good stuff and scored some good goals.
"The lads have played a lot of football and have got a few niggles, so we reduced the game by 10 minutes and played two 40-minute halves.
"Ryan Humphreys hasn't been at his best in pre-season so far, so it was good to see him get a hat-trick. Bradley Mason and Ryan Thompson were both very good at centre half and Antonie Boland also did well."
The Academy boys are back in action against Eric Kinder's Carlisle United this Saturday at Brockhall.