Flitcroft, 38, handed the job until the end of the season after taking on the role of caretaker two weeks ago, spent over five years as assistant to previous manager Keith Hill, first at Rochdale before the pair moved to Oakwell in June 2011.
Hill was sacked by Barnsley on December 29 and some fans wanted a complete break from the previous management regime, but when new Bristol City manager Sean O'Driscoll and Inverness boss Terry Butcher turned down the job, the Oakwell board handed Flitcroft his chance after he steered them to back-to-back wins over Burnley, in the FA Cup, and derby rivals Leeds.
"By his own admission, David is a different character to Keith and is different in terms of how he goes about things," said director Don Rowing.
"He has his own way of doing things - you have to have if you want to be a football manager.
"We believe David has earned his chance because of what the team have done over the last two or three weeks, on the playing side he's made the team more effective in the right areas."
O'Driscoll, sacked by Nottingham Forest on Boxing Day, was named as successor to Derek McInnes at Bristol City on Monday, while Butcher, who has led Inverness up to second place behind Celtic in the Scottish Premier League, opted to stay north of the border.
"A couple of people turned us down," Rowing added: "The two guys we did interview in the first instance - and we wanted to go for someone with experience given the circumstances - were proven managers in their own right and the reasons why they did not take on the job are acceptable.
"Those reasons were nothing to do with Barnsley Football Club. O'Driscoll wanted three weeks before he made a decision and Butcher, understandably, has unfinished business at Inverness and wanted to stand by his chairman."