Kerr is one of the UK's highest qualified and experienced female coaches. The 59-times capped Scottish internationalist will lead the continued development of the men's football club, and carry out head coaching duties for the football scholarship programme at Scotland's University for Sporting Excellence.
Kerr will also begin studying for a MSc in Sports Management at the University next month.
With the University's 1st XI now playing in the Scottish Lowland League, in effect the fifth tier of Scottish senior football, Kerr becomes the first female in the UK to manage a senior professional men's team.
One of only four women in the UK to hold the acclaimed UEFA Pro-Licence Award, Kerr previously managed Arsenal Ladies in the English Women's Premier League, leading them into the European Champions League, as well as gaining FA Cup success. Prior to working with the London-based club she was the Scotland Women's National Under-19 coach.
Kerr is delighted with the new appointment and her first leading position in the men's game. She said: "I am extremely excited to be given this opportunity to lead the men's performance programme at Stirling.
"I am looking forward to transferring my knowledge and experience as an international player and coach - to develop further the players and the programme at Scotland's University for Sporting Excellence."
She added: "I have always had a desire to work in the men's game and the University of Stirling - a very forward thinking educational establishment - has given me the ideal opportunity to do so."
Raleigh Gowrie, the University's Sports Performance Manager, said: "I'm very pleased that Shelley Kerr has agreed to base herself at Stirling and take forward the development of football at the University.
"The University of Stirling has made history by appointing Shelley as the first female manager in British men's senior football and we are delighted.
"Not only is Shelley a well-qualified and successful coach, she holds a strong vision of club development and a willingness to enhance the sporting experience for our students. I'm confident she will add great value to our successful programme and complement a strong team.
Alongside her lead role in men's football, Shelley is interested in the development of women's football at Stirling. The University has teamed up with Scottish Women's 1st Division side, Falkirk Ladies FC, to offer scholarships in the women's game, with a desire to have their students playing in the Premier League within the next two years.
Shelley said: "Stirling's innovative scholarship programme in partnership with Falkirk Ladies has the potential to revolutionise the women's game in Scotland and, in due course, offer strong competition to the teams dominating the domestic club game currently. There is a lot to be excited about."
The University of Stirling has awarded football scholarships since 2008. Since then more than 100 awards have been made to help talented young players combine their football development with studying for a higher degree.
The programme has helped bring competitive success to the University, with the 1st XI winning the British Universities' Premier League (North), the British Universities' Championship and the Scottish Lowland League Cup last term.
A second-place finish in the inaugural Scottish Lowland League gained the students entry into this season's Scottish FA Cup. A number of players from last year's successful side have either graduated or moved into the senior professional game in Scotland, ensuring that this will largely be a year of transition for the students as well as for Kerr.