The Reds reserves lost again in a game which was marred by a serious injury to young striker Ashley Scothern.
Scothern was carried off the pitch on 62 minutes with a suspected fractured leg. Ashley has missed most of the last two years after twice breaking his leg.
The Reds took the lead on 43 minutes as Griff Jones turned well after a pass from Steve Hayward and fired into the bottom corner.
Second half goals from Paul Hayes and Andy Parton gave Scunny the win.
Barnsley Line-up: Alcock, Burns (Harban 45), Williams (Laight 59), Atkinson, O’Callaghan, Hayward, Neil, Wroe, Scothern (Oldham 64), Jones, Rankin.
Subs: Flinders, Tonge.