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Initial seasons (2009–2013)

Chattanooga FC was founded in 2009 by Tim Kelly, Krue Brock, Marshall Brock, Paul Rustand, Sean McDaniel, Daryl Heald, Hamilton Brock, Thomas Clark, and Sheldon Grizzle to play in the National Premier Soccer League (NPSL), the fourth tier of the American soccer pyramid and considered roughly equal to the USL Premier Development League. The team completed its inaugural season third in the Southeast Division with 4 wins and 3 losses.

After the struggles of its first season, Chattanooga FC's run in 2010 included winning the conference and it got them to the NPSL finals. The season ended with a loss in the 2010 NPSL Championship game to the Sacramento Gold by a score of 3–1. After a disappointing 3rd-place finish to the 2011 season and missing the playoffs, Chattanooga FC came back stronger than ever in 2012, taking 1st place in the newly created South Southeast Conference West, and defeating the reigning NPSL champion Jacksonville United FC 4–1 in Jacksonville to clinch it. Because of a collapse of the South-South Central Conference structure, a one-game playoff to determine the South Conference Champion was held with the Georgia Revolution, the victors of the South Southeast Conference East in Conyers, GA. Chattanooga won the game 1-0 on Luis Trude's 72nd-minute goal to advance to the 2012 NPSL National Finals in San Diego, CA. After defeating the Bay Area Ambassadors 3–2, and advancing to the NPSL Championship game, Chattanooga lost again in the title game 0-1 to FC Sonic on a header in the 78th minute. This was the 2nd NPSL Championship game that Chattanooga FC lost.

Chattanooga FC's 2013 season started with the expansion of the South Region into four divisions, with Chattanooga placed in the Southeast Division of the South Conference with 5 other teams. Chattanooga again prevailed at the top of the division, but because of one loss, had to go on the road for the Regional Playoffs. Chattanooga traveled to Tulsa, Oklahoma to face the undefeated and top seeded Tulsa Athletics who won the South Central Division. After a 0–0 draw, the match went to penalty kicks. Keeper, Greggaa Hartley, converted an incredible 3 saves in 3 chances, and Chattanooga made all 3 of their chances to advance to the Regional Final in Richmond, VA. Chattanooga FC lost the Regional Final 1-0 to eventual NPSL champions RVA Football Club. For the 2013 season, 4 Chattanooga FC members were selected to the 2013 All-NPSL Team - more than any other team. Those players were: GK Greggaa Hartley, DF Andrew Stewart, DF Nicholas Chase, and MF Fynn Glover. MF Thibault Charmey was also included in the NPSL Supporter's XI along with Hartley, Stewart, and Glover.

Continued success and Hank Steinbrecher Trophy (2014–2017)

2014 started with former Chattanooga FC player Mark Sherrod being drafted by the Houston Dynamo of Major League Soccer in the second-round of the 2014 MLS SuperDraft. For the season, Chattanooga FC launched a Women's Soccer Team in the WPSL for the first time. In their inaugural season, the women's team finished 5-3-2, for third in the Southeast. Chattanooga FC's regular season started off slow, but ended with 5 straight wins to close the season on top of the division once again by goal difference over the Atlanta Silverbacks Reserves. For 2014, the playoff format changed to a playoff to determine the Southeast Champions. The playoff was hosted by Chattanooga as the regular season champions. Chattanooga defeated Nashville FC 6-1 and then the New Orleans Jesters 4-0 to advance to the Regional Playoffs.

Although given the lowest seed in the Regional Playoffs, Chattanooga also played host to the Regional Playoffs. Chattanooga went on to defeat top seeded Miami United F.C. 2-0 and the Tulsa Athletics once again 2–0 in a rematch of 2013's Regional Match. Chattanooga would next host the Sacramento Gold in a rematch of the 2010 NPSL Championship game. They would end up rallying from an early 0–1 deficit to win 4–1, advancing to the finals for the third time in the club's existence. Chattanooga FC lost to the New York Red Bulls U-23 3–1. Forward Luke Winter and keeper Gregory Hartley were named to the All-NPSL squad, with Hartley also taking home honors with the NPSL Golden Glove award. Head Coach Bill Elliot was also awarded the Alexander Arellano Memorial Trophy for top NPSL Coach.

The 2015 season saw 2014 standout midfielder Niall McCabe sign with Louisville City FC in March. Chattanooga FC was also selected to host the US Soccer Amateur Championships on May 29–30, also known as the Hank Steinbrecher Trophy, in a competition matching the previous years winners of PDL, NPSL, and USASA Open and Amateur Championships. In May, CFC opened league play winning the first two matches on the road in Georgia. U.S. Open Cup play started at home against Ocala Stampede in the first round. After a late goal by Luke Winter to tie the game in regulation, the game went to extra time, with Gregga Hartley saving two penalties, and converting the winning one himself. Hartley was named TheCup.us 's Player of the Round.

The 2nd round of the Cup was away at Wilmington Hammerheads, and went to penalty kicks again after 1–1 in regulation. Chattanooga converted all 5 kicks, and saved one of Wilmington's to advance to host Atlanta Silverbacks once again in 3rd Round. Chattanooga FC took the lead late in the game on a Luke Winter header, but a controversial penalty was called just a minute later. Atlanta equalized and won the game in Extra Time, 2-1 the final. Just 2 days after the defeat Chattanooga FC hosted the Maryland Bays, the 2014 USASA Open Cup Champions, for the opening game for the Hank Steinbrecher Trophy tournament. Chattanooga won that game 2–0, and the next day defeated the Michigan Bucks, the 2014 PDL season Champions 3-0 to win the trophy, Chattanooga FC's first. On August 8, 2015, Chattanooga FC and Finley Stadium hosted the NPSL National Championship between CFC and New York Cosmos B. The game drew a U.S. amateur soccer attendance record with 18,227 fans witnessing a thrilling match won by the Cosmos, 3–2 in extra time. In 2016, Chattanooga FC won all of its games 9-0 and was first in the Southeast Division. The team advanced to the Southeast Conference playoffs, where they beat Memphis City FC 2–1. After the win over Memphis, Chattanooga FC managed to advance to the Regional Finals of the NPSL Playoffs, where they won in a penalty shootout to Miami United FC 5–3.

In January 2017, Chattanooga FC announced a partnership with VfL Wolfsburg, which plays in the German Bundesliga, and has plans to have international friendlies with the team.

Transitioning to professional status (2018–present)

A professional USL League One franchise, later named the Chattanooga Red Wolves, was established in 2018. Chattanooga FC accused the new team of trying to take over the local market after they hired then-current general manager Sean McDaniel. The Red Wolves also unsuccessfully attempted to arrange a lease at Finley Stadium and takeover of Chattanooga's youth academy. The city's women's team was transferred to the Red Wolves organization in 2019.

On November 15, 2018, the NPSL announced that it was creating a new, fully professional division and that Chattanooga would be one of its founding teams. In anticipation of moving to a professional roster and schedule, Chattanooga began a fan ownership initiative that was partially modeled after the Green Bay Packers. The initiative raised more than $800,000 with almost 3,000 new owners for the club from all 50 states and 25 different countries.

On August 15, 2019, it was announced that Chattanooga FC would instead join the National Independent Soccer Association. In preparation for the team's move to the professional ranks it was announced that Jeremy Alumbaugh, formerly the general manager of Saint Louis FC, as the team's managing director, while Bill Elliot would transition from his role as coach to Technical Director and Peter Fuller would take over the head coach role full-time.

After having three years of success in NISA, winning all three Independent Cups and finishing first in the 2023 NISA season, Chattanooga FC announced that starting in 2024 that they would join MLS Next Pro, the other third tier professional soccer division in America, which serves as a reserve league for Major League Soccer. Chattanooga FC will become the fourth independent club to become part of MLS Next Pro.