They were second in the table at the time, behind leaders Tranmere on goal difference, and Flynn maintained the promotion push leading to them taking the title last Saturday after a dramatic win at Brentford.
It was assumed he would continue as manager but that looked to have taken a knock earlier in the week when Doncaster extended his contract by two weeks to ensure he remained on the payroll while plans were put in place for next season.
Then, today, came news that Flynny has made the decision himself to step down to return to the area of player development.
Doncaster confirmed today: "Following the end of the season, Brian Flynn has approached the club and expressed a desire to return back to what he sees as his passion in the development and recruitment of players.
"I line with this the owners have offered Brian a senior role within the club developing and supporting whoever is to manage the side as it goes into the Championship. Brian will be involved in the search for a new manager and new players for the challenge ahead in one of the most competitive leagues in the world.
"Brian will go down in history after the dramatic end to the season and the club see Brian as the ideal man to lead the development of Doncaster as a force both at senior and youth level."
Since the initial statement it has been reported that Flynn, who said after last week's win: "Who would not want to manage in the Championship?" has now accepted the role of Director of Football at Doncaster.
They are expected to announce his successor as manager within the next two weeks and the early favourite is former Oldham manager Paul Dickov.
Source: Clarets Mad