The Sporting Equality Fund will be spent trying to close the gender gap that emerges in early teenage years.
During this period 71% of boys say they are active in sport compared with 51% of girls.
First Minister Nicola Sturgeon said the aim was to increase participation, engagement, and promotion of women in sport.
Details of the fund were being set out at the Ladies Scottish Open Forum: Leadership in Business and Sport event.
Ms Sturgeon said: "We've seen some good progress in recent years, and it's encouraging that activity levels amongst teenage girls are increasing.
"However, there is still a gender gap in sports participation and physical activity levels. There's also a shortage of women involved in sport from grassroots right up to elite level."
She added: "We look forward to working with sportscotland and others over the summer to take this forward and will be announcing more details later in the year."
Scottish golfer Catriona Matthew said: "As a mother to two young girls, I am delighted to hear about the Sporting Equality Fund which aims to get more women and girls actively participating in sport.
"Keeping fit and healthy is so important in terms of health, wellbeing, mental strength and social mobility."
Sportscotland's chair Mel Young welcomed the news, saying the body was committed to building a "world-class sporting system" for everyone in Scotland.
A £300,000 scheme is being set up to increase women's engagement in sport in Scotland.