Flynn took over as caretaker manager at the beginning of January following Dean Saunders' departure to Wolves and was later handed a deal until the end of the season.
The former Wales Under-21 boss led Rovers to the League One title with a dramatic 1-0 win at Brentford on Saturday.
However, it remains to be seen whether the 57-year-old will be the man in charge when the south Yorkshire club kick-off their Championship campaign in August.
"We've extended Brian's contract by a couple of weeks so he's still getting paid," Doncaster chairman John Ryan told BBC Radio Sheffield.
"I'm going to sit down with the major shareholders on Tuesday and discuss a lot of peoples' futures.
"It isn't just Brian, there are a lot of other people out of contract too."
Doncaster sealed an immediate return to the Championship thanks to James Coppinger's injury-time winner against Brentford, who seconds before had missed a penalty that would have sent them up at Rovers' expense.