He replaces Julie Chipchase who left to manage Leeds, and leaves behind a coaching role at Hull City.
Doncaster Rovers Belles were formed ahead of the coming season after a merger between Doncaster Rovers men's team and Doncaster Belles women's team enabling them to share facilities.
Belles general manager Mick Abrahams said: "John is a highly experienced professional with a great reputation. He was my first choice when we knew Julie was leaving, but we did our homework on him and everybody we spoke to gave him a glowing reference.
"When we had our meeting with him earlier this week Karen Walker (club captain) in particular was highly impressed with his ideas and his stratergy for moving the club forward. I think he'll give us that extra ten per cent we've been lacking."