Malcolm Press, pro vice-chancellor for research and knowledge transfer at the University of Birmingham, will take up the top post at MMU on 1 June.
He said the university was well placed to take advantage of new opportunities for Manchester offered by greater devolution.
John Brooks, MMU’s existing vice-chancellor, is retiring after 10 years in the job.
MMU had originally announced that Professor Brooks would retire this month. However, the first recruitment process to find a successor had to be aborted after the university’s governors rejected the selected candidate in the summer – with the chair of governors then resigning.
Malcolm Edge, who was appointed Manchester Met’s chair of governors in June 2013, is thought to have been part of an appointment committee that selected a candidate to be vice-chancellor.
When that choice was rejected by the university’s board of governors, Mr Edge is understood to have felt that he could no longer count on the confidence of the board and left, having been in the post about a year.
Vanda Murray, former deputy chair of governors, stepped up to become chair.
Professor Press, an ecologist, studied for his PhD and worked as a lecturer at the University of Manchester.
He said: “The university is superbly equipped to take full advantage of the new opportunities that Manchester will gain from greater regional devolution and investment in the North.”
He added: “I am looking forward to returning to a great city where I’ve both studied and worked, to lead an institution that deserves to be the UK’s best modern university.”
Ms Murray said: “MMU has become the UK’s most popular undergraduate university with major investments in all aspects of university life, including its infrastructure and facilities, under the leadership of our vice-chancellor Professor John Brooks.
“The platform is now set for us to take MMU to the next stage of its growth and development on a regional, national and world stage. As the unanimous choice of the board of governors, we are confident that Professor Malcolm Press is the ideal person to lead us forward.”
Professor Brooks said the appointment was “an excellent decision” by the board. “Professor Press has an outstanding academic track record and broad experience of the research-led part of the sector which will strengthen MMU and help it to deliver its academic vision,” he added.