He succeeds Carla Ward, who resigned as Birmingham boss in May after steering the side clear of relegation from the Women’s Super League, and will link up once more with former Glasgow City players Christie Murray, who captains the Damson Park side, and forward Abbi Grant.
The former Scotland international took the reins at Broadwood in July 2015 and led the side to six league titles and two Scottish Cup wins during his tenure.
Booth also took City to the quarter-finals of the UEFA Women’s Champions League for just the second time during the 2019/20 season.
Speaking to Glasgow City’s website, Booth said: “I would just like to say thank you to all of those who have been part of our incredible journey over the last six years at Glasgow City FC; some absolutely incredible people working so hard for this great club.
"A huge thank you to the board and of course Laura Montgomery and Carol-Anne Stewart for giving me the opportunity to be part of something special.
"I will never forget the players that I have worked with at City and I want to thank them for all their hard work and dedication over the years.
"I wish the club every success going forward.”
Chief Executive Laura Montgomery added: “Scott leaves with our very best wishes. We have had amazing success together and we have worked really well as a partnership.
"His dedication to the job has been faultless and he got our club and our ethos the moment he joined Glasgow City. He is a great coach and a great person and I wish him the very best in his new post.”
City have started the process of recruiting Booth’s successor.
Birmingham City Women made the headlines in April when the entire first-team squad put their names to a formal letter to the club's board, with a list of complaints about working conditions including concerns about medical support, travel provisions, and access to gyms and changing facilities.