Ferguson, the son of legendary Manchester United boss Sir Alex, announced his decision via the League Managers Association.
His statement read: "Following recent discussions and meetings with the board I have decided to resign from my position as manager of Doncaster Rovers Football Club.
"I'm disappointed to have made this decision as I have enjoyed my time at the club and was looking forward to the new season, but I felt I had no alternative.
"I would like to thank the board for the opportunity and I am grateful to the players, staff and fans for their support. I wish the club all the best in the future."
Ferguson won 55 of his 145 games in charge of 'Donny', with a win percentage of 37.9%.
His final season in charge saw Ferguson guide the Yorkshire side to a safe 15th-placed finish in the English third division, having secured automatic promotion from League Two the previous campaign.
June 4, 2018