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Charleston Battery was formed in 1993 by an ownership group of local soccer enthusiasts led by Tony Bakker, a native of London who had relocated his software company Blackbaud to the Charleston area in 1989. The club hired experienced college coach and University of South Carolina graduate Tim Hankinson to develop the team, and Battery started as a member of the USISL, which eventually evolved and came to be known as the USL in 1995. The Battery won their first league championship in 1996 under Portuguese manager Nuno Piteira, defeating the Charlotte Eagles 3–2 in the final. In 1997 Charleston became one of the original clubs of the newly branded A-League (later the USL First Division).

In 1999 Charleston Battery moved into what is now known as MUSC Health Stadium, becoming the first non-Major League Soccer professional club in the United States to build its own stadium, and forged a reputation as one of the country's most well-established lower division clubs. The Battery hired veteran English coach Alan Dicks and signed many experienced domestic players such as Paul Conway, Dan Calichman and Eric Wynalda while also bringing in notable foreign signings such as Terry Phelan and Raúl Díaz Arce. In 2001 Dicks was replaced by fellow Englishman Chris Ramsey, who led Charleston to the A-League championship in 2003 with a 3–0 victory in the final over Minnesota Thunder in Charleston. Following Ramsey's departure in 2004, the club promoted longtime player and assistant coach Mike Anhaeuser to be the club's new coach.

In 2008 Charleston Battery reached the Lamar Hunt US Open Cup final for the first time, playing against Major League Soccer team D.C. United at RFK Stadium. In the final the Battery conceded an early goal but bounced back with a quick-fire equalizer through an Ian Fuller goal, assisted by Chris Williams. Later in the half Lazo Alavanja hit the post but at half time the scores were tied at 1–1. At the start of the second half Charleston conceded early again, but in the final seconds of extra time Marco Reda put the ball in the back of the net for Charleston, only to have his goal controversially disallowed as offside. D.C. United would go on to win the match 2–1.

In 2010 Charleston was invited by several other USL clubs to join the breakaway league eventually known as the North American Soccer League, but Battery chose to remain in the USL system and self-relegate to the USL Second Division, which eventually became the chief USL professional division. In their first third division season in 2010, Charleston led the league standings for the entire year and went undefeated at home. Charleston defeated the Richmond Kickers 2–1 in the final to claim the club's third league championship. Lamar Neagle was named the USL-2 league MVP and lead the league in scoring with 13 league goals. Anhaeuser was named the league's coach of the year, his second time receiving the honor. In 2012 Charleston Battery won their fourth league title in club history, defeating local rivals Wilmington Hammerheads 1–0 in the final. Micheal Azira scored a 74th-minute winner after Jose Cuevas slipped a pass to him on the left side of the penalty area.

In recent years Charleston Battery have had loan affiliations with several Major League Soccer clubs, beginning with a one-year deal to become the USL Pro affiliate of Vancouver Whitecaps FC in 2014. For the 2015 season, Battery signed a one-year deal to affiliate with the Houston Dynamo. On January 15, 2016, it was announced that the club would be partnering with the Atlanta United FC for the 2016 MLS season prior to Atlanta's entry to MLS in 2017.

In February 2016, it was announced that longtime majority owner Tony Bakker had sold the club to B Sports Entertainment, an investment group led by local tech executives. Club president Andrew Bell and coach Mike Anhaeuser remained in charge of team operations after the ownership transition. In early 2018 it was announced that Bell would be leaving the club to take over operations of an announced USL expansion club in Memphis, Tennessee, ending a two-decade career in the Charleston front office. Bell was replaced by club operations officer Mike Kelleher.

In October 2019, it was announced that B Sports Entertainment had sold the club to Rob Salvatore of HCFC, LLC with a move to Patriots Point Soccer Complex in Mount Pleasant.

At the conclusion of the 2021 season, the Battery announced on November 1, 2021, that the club and Mike Anhaeuser had parted ways. Anhaeuser joined the Charleston Battery as a player in 1994, and switched into a coaching role in 1999. In 2004, he was named head coach of the club and led Charleston Battery to a U.S. Open Cup Final appearance in 2008 as well as two USL Championships in 2010 and 2012.

On December 20, 2021, Battery announced that they had hired Conor Casey as head coach. However, on October 12, 2022, with one match remaining in the season and the Battery near the bottom of the Eastern Conference standings, the club and Casey opted to part ways by mutual agreement. Assistant coach Dennis Sanchez was named interim head coach while a search for a permanent replacement began.

On November 17, 2022, Battery announced that they had hired Memphis 901 FC head coach Ben Pirmann for the same position in Charleston. Pirmann was named the 2022 USL Championship Coach of the Year after leading Memphis to a 2nd-place finish in the Eastern Conference and a spot in the conference semifinals.