Danny Wilson’s men rarely threatened during a disappointing second-half effort and were booed off at the final whistle.
Fleetwood came from behind to lead 2-1 at the interval at Oakwell, the hosts having gone in front after just five minutes.
Leading scorer Conor Hourihane fired in a wicked free-kick that was only parried by goalkeeper Chris Maxwell right into the path of centre-back Peter Ramage, who fired home.
However, the visitors were level just nine minutes later when full-back Conor McLaughlin pounced on a poor attempt at a clearance by Lewin Nyatanga, and smashed home into the top corner of the net.
What proved to be the winner for the Cod Army came 11 minutes before the break, when Liam McAlinden was left free to poke the ball home from four yards.
Kane Hemmings went close twice for the hosts, and Nyatanga headed narrowly over, but it was not the Tykes’ night.
Barnsley: Turnbull, Crainie, M’voto (Smith, 46), Ramage, Nyatanga, Scowen, Hourihane (Jennings, 77), Pearson, Lalkovic (Kiwomya, 60), Hemmings, Waring. Unused substitutes: Davies, Holgate, Bailey, Lita.
Fleetwood Town: Maxwell, McLaughlin, Roberts, Jordan, Crainey, Hughes, Evans, Morris, Haughton (Sarcevic, 63), McAlinden (Hunter, 81), Ball (Murdoch, 73). Unused substitutes: Springthorpe, Pond, Dobbie, Hornby-Forbes.
Referee: D Coote (Notts).