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The club was founded in 1999 as Shepshed Foxes by Gail and Paul Fox, who wanted to give girls in the surrounding area an opportunity to play football, before becoming Loughborough Foxes in 2002.

After playing in local leagues for much of the first 15 years of their history, Loughborough were promoted to the FA Women's Premier League Northern Division (the 3rd tier of women's football) for the first time in 2015 from the Midlands Division One but would suffer relegation back to the 4th tier after just one season. The Foxes returned to the now renamed FA Women's National League in 2018 having secured promotion and the Midlands Division One title with a record of 21 wins and 1 draw from 22 games.

In January 2019, Loughborough Foxes player and junior team coach Molly Webb died aged 25, with Director of Football Steve Wilkinson describing her as "a joy to spend time with; she was vibrant, enthusiastic, a motivator and someone you want in your team whatever the situation.". The Foxes would end their first season back at the third tier of women's football in 7th place in the 2018–19 FA Women's National League Southern Division before being realigned to the Northern Division for the following season.