Reading FC began an association with women's football when it affiliated with Reading Royals LFC (previously Twyford Comets) in 1988. In May 2006, Reading ended this affiliation and started their own women's team, Reading FC Women. In their very first season they achieved a Southern Region Women's Football League and Cup double and were promoted to the South West Combination Women's Football League. They followed this with an unbeaten 2007–08 League season to gain promotion to the Premier League Northern Division (in which they competed due to an overload at the Southern).
After finishing sixth in the Northern Division, Reading were transferred to the Southern Division for the 2009–10 season. In 2010 they won their last four games of the season to finish runners–up to Barnet and secure promotion to the FA Women's Premier League National Division.
On Sunday 3 April 2011 Reading Women successfully defended the Berks and Bucks County Cup trophy, cruising past Milton Keynes Dons 3–0 in the final.
Their first season in the FA Women's Premier League National Division (the second highest league, following the formation of the Women's Super League) saw Reading finish third. In March 2012 Reading lost top goalscorer Nikki Watts to WSL club Bristol Academy. They finished 9th in the National Division in the 2011–12 season, resulting in their releagtion back to the Southern Division for the 2012–13 season.
In 2012/13 Reading FC Women won the FA Premier League Southern Division by eight points and a goal difference of 41, while both the first and reserve team managed to retain the County Cup.
Reading FC Women's top scorer in 2012–13, Fran Kirby, was rewarded for her campaign by being named as Player of the Season – as well as receiving a call up to play for Great Britain in the World University Games in Russia. Kirby surpassed the 30-goal mark this season. The striker was also selected for an England under-23s Camp.
From 2014 Reading FC Women have been granted to play in the FA Women's Super League 2.