The club was formed in 1897, and starting playing in the Aldershot League. The club then moved to the Surrey County Intermediate Leagues after World War two, where they were to become champions at the end of the 1949–50 campaign. They then followed this success in the next three following seasons, with two more wins in the 1951–52 and 1952–53 competitions.
For the 1972–73 season, they joined the Hampshire League, starting in Division four, which they won at the first attempt. The club had further success when they won Division three at the end of the 1975–76 competition to gain promotion to Division Two. The club remained in Division two until the end of the 1980–81 season.
The 1981–82 campaign saw the club join the Combined Counties Football League, starting in the West Division, which then merged with e Eastern Division to form a single division the following season. The club remained in the division until the end of the 1989–1990 competition , where finishing third they left the league to play in the Isthmian League.
For their first season in the Isthmian League, they started in Division Two south, and at the end of the season were placed in Division Three upon re-organisation of the league. Their first season in the Isthmian league also saw the club make their debut in the FA Cup losing to Windsor & Eton in the First Qualifying round after beating Haywards Heath Town in the previous round. The club stayed in the Isthmian league Division Three until the end of the 1995–96 campaign, when they decided to drop back down to the Combined Counties League, due to the higher costs of competing in the Isthmian league.
In the 2000–01 season the club won the Combined Counties League and completed a double when they beat Walton Casuals, in the final of the Premier Challenge Cup.
The club won the Southern Combination Cup Final 4–0 against Chessington & Hook United under manager Koo Dumbaya. On April 23, 2010, Cove FC beat Bedfont 2–0 after extra time in the EL Records Combined Counties League Cup. Cove also reached the Aldershot Senior Cup final when they beat Farnborough in the semi final, but lost to champions Fleet Town in the final.
Early into the 2012/13 season Cove parted ways with then manager D.Thomas, this paved the way for the rookie managers Dan Reeves 28 and Anthony Millerick 30 to take the helm as joint managers. This appointment started with the clubs first back to back clean sheets of the season, and infact 4 back to back wins with no goals conceded was seen. This progressed throughout 2012 with Cove entering the new year in 5th position. As 2013 kicked off Cove have further gone from strength to strength. With the 1st 2 months of 2013 remaining unbeaten, and currently occupying 3rd spot. It was announced in the Farnborough news and Mail on 21/02/2013 that Cove have now emerged as shock title contenders.