Munro, 52, who will become head academy coach for Glasgow & West, has been in charge of Scotland since June 2015 when he became their first full-time head coach.
He led his side to victories against Italy and Wales in the 2017 Six Nations and achieved the first victory against Ireland in the competition, away from home, last year.
Munro, pictured, said: “I’ve really enjoyed working with this group of players and seeing the improvements they have made. I am proud of how much they have all developed individually and as a team.
“Increasing the level of coaching and amount of training regionally, along with the increase in national camps and competitive fixtures has helped hugely with this development.
“There have also been some fantastic highlights during my time involved most notably achieving our first Six Nations win in 35 attempts along with our first away win in the same competition last year against Ireland.
“Given the passion and commitment the players show when representing their country and their collective desire to continue to improve I have no doubt that further success awaits Scotland Women’s rugby.
“I would like to wish them all the very best for the future.
“The new Academy position will provide an opportunity to work with different players who are at a key stage in their career, making this an attractive role to take on and one I am looking forward to.”
The appointment came in January, but Scottish Rugby and Munro agreed he would lead the team in the Six Nations. Scotland ended that campaign by losing 80-0 to England at Twickenham on Saturday.