City chairman Adam Pearson announced today that the Dane has signed a three-year contract.
He said: "I am delighted that Jan Molby has joined us.
"I wanted to appoint a manager who craves for success for this club as much as myself and the supporters.
"He understands and knows about the Third Division but also has a hunger to return to the top levels of football.
"He now has a chance to assess the squad, highlight their strengths and weaknesses and recruit key players for the start of next season.
"We will invest again this summer in quality signings who will be integral in achieving Third Division success and they will be added to what I believe is already a talented squad but one which needs to perform to potential next season.
"Promotion winning teams are not built over night but I feel the nucleus is there for Jan to add to for next season and I'm sure everybody involved with club will join me win welcoming him to Boothferry Park."
This will be the Dane's third club as a manager. He previously took Swansea City to the Division 3 play-offs, and Kidderminster Harriers to promotion from the Conference, before resigning recently.
He also had a distinguished playing career, as a championship-winning midfielder at Liverpool and on the international stage with Denmark.