Sheila Begbie, a former Scotland international footballer, will leave the SFA after a 16-year stint to take up her new post in August, it was announced on Thursday.
Scottish Rugby said in a statement: "Scottish Rugby is delighted to announce the appointment of Sheila Begbie MBE to the newly-created position of head of women's rugby."
Begbie said: "I think what I'll bring from football is a blueprint of success because we've had lots of successes in the women's game."
She will report to director of rugby Scott Johnson, who said: "It's a wonderful appointment. Sheila has had a great career in Scottish women's soccer and this shows our intent to make women's rugby a priority and how important this aspect of the game is to our organisation."
SFA chief executive Stewart Regan rued the loss of Begbie, saying: "Sheila will be a loss to the Scottish FA. Her drive, commitment, expertise and connections across sport and politics have helped the women's game take huge leaps forward at all levels."
The SFA has begun the search for a new head of women's football, advertising the position on its website.
A possible contender could be former Scotland player Shelley Kerr, who stands down as manager of Arsenal Ladies following Sunday's Women's FA Cup final.