The 39-year-old, his assistant Micky Mellon and first-team coach Martin Scott all put pen to paper on their respective one-year rolling contracts at a press conference.
The Tykes' new management team had been installed until the end of the season following the sacking of former boss Keith Hill at the end of December and defied the odds to keep the club in the Championship after a thrilling run-in.
"We feel we can win football matches," said Flitcroft, who won eight of his first 10 games in charge. "We've beaten some of the very best that the Championship had to offer last season.
"This season it's a different league with different teams. There are 10 teams who have parachute payments, but what we had to make right was the management team that made us successful last season and that's Micky Mellon and Martin Scott, who played a massive part in out upturn when we took over.
"I wanted to make sure these two lads got their future sorted because it is a new era, there are some things we'll be trying to do differently at the club and the way we want to manage this club is key now."
Flitcroft said discussions with the board about next season's playing budget had been on-going since the last-day draw at Huddersfield ensured another season in the second tier.
"We've signed now because things are looking right at the club. We've got to keep progressing and evolving.
"We'll get players in if they're right for Barnsley. If they're the right people for this town then we'll try and sign them. We must try and attract the right type of player.
"There have been lengthy discussions with the board about the playing budget over the last two weeks, we've not stopped since the Huddersfield game, planning and preparing."