The club was founded in 1920 under the name Loughborough College. They joined Division Two of the Leicestershire Senior League in 1966, where they remained until 1972. The club then left Senior football, and did not return until 2007 when they were promoted to the Premier Division of the Midland Combination. In 2008–09 they won the league's Premier Division, and were promoted to the Midland Alliance. The Scholars ground shared at fellow local side Loughborough Dynamo until moving into the new Holywell Park, Loughborough University Stadium.

In 2011 the club beat Boldmere St Michaels 4–2 to lift the League Cup at Walsall's Bescot Stadium, then won the trophy again the following season when they beat Tipton Town 2–0.

With the reorganisation of the Step 5 leagues in 2019, Loughborough Students FC were moved in to the United Counties League. Reaching the final of the Leicestershire and Rutland FA Senior Cup Final only to lose out in the final to Step 3 side Coalville Town FC

In the 2021–22 season the Scholars were crowned BUCS National Champions for the first time in nine years and were semi-finalists in the FA Vase, losing away to Littlehampton Town, their best ever performance in the Vase. In 2022–23 they narrowly missed out on an inter-league play off place. In the 2023–24 season after finishing third in the league, they secured promotion via the playoffs beating Skegness 7-0 in the Playoff final gaining promotion for the first time to non-league Step 4, and were runners up in the Leicestershire and Rutland County Cup.