Chris O'Grady and Norwegian Marcus Pedersen, on loan from Vitesse Arnham, put the home side 2-0 up at the break and they restricted derby rivals Huddersfield to a goal from James Vaughan after the break, weathering pressure from the Terriers.
Flitcroft said: "It's really pleasing to get three points on the board after going toe to toe with an in-form Huddersfield team and putting in a good performance.
"We've been knocked and not won games we possibly should have won so I'm pleased that we've come out on top today. All the players deserve credit.
"I get encouraged every day by this group. The easiest way to feel when you're losing is to lose belief, but I won't do that with these players.
"We're going to keep working with them and keep believing in them. I do believe we've got good people in the dressing room.
"The players were fighting for the cause and fighting for each other and I thought they were excellent."
The pressure applied by the visitors paid off when Adam Clayton picked out Vaughan with a fine through-ball and the in-form striker shot low past goalkeeper Mike Pollitt.
"We knew there would be spells when Huddersfield would be dominant," Flitcroft said. "They threw players up front but we were resilient and withstood anything that they threw at us.
"Chris (O'Grady) was excellent. He's someone who carries the fight and holds the line. His goal was sublime - a great finish.
"Chris sometimes doesn't get the credit that he deserves. His link-up with Marcus Pedersen was superb and I'm convinced they're going to be a threat in this league."
Flitcroft could be active in the transfer market before Monday night's deadline.
"We're continually looking to improve the playing staff and we probably need to bring a couple of players in. We're just waiting for the right ones to drop in," he said.
Huddersfield manager Mark Robins had no complaints about the scoreline, admitting his side were second best on the day.
Robins said: "There are no qualms about the result. In the first half we were overran but in the second half we were better.
"Barnsley were committed and scored a couple of goals before we got out of the blocks.
"At half-time we had a conversation and things changed a little bit for us. We looked more likely to score in the second half.
"We created a number of chances and on another day we could have won the game.
"It was a great ball from Adam Clayton for the goal and James had another couple of chances to score.
"Inevitably, Barnsley dropped 10 yards back after we scored and we just needed a bit of guile.
"There's no substitute for working hard and trying to close people down and they did that better than us. That can't happen again."