The predecessor of FC Tokyo, Tokyo Gas Football Club, was founded in 1935. The team, which played in the Tokyo Metropolitan League, was promoted to the Kanto League in 1986 and achieved a strong 4th place finish in its first year. In 1991, they won the National Regional League Championship Tournament and were promoted to the JSL Division 2. From 1992, they joined the JFL, and while watching the launch of the J League in 1993, they consistently maintained a top position in the JFL from 1995 onward. In the 1997 Emperor's Cup, they made a remarkable run by defeating three J League teams in a row to reach the Semifinal Round, and in 1998, their final season in the JFL, they achieved their long-awaited first championship.

In 1999, the year the team renamed itself "FC Tokyo" and entered the J.League Division 2 (J2), they defeated J1 teams three times in a row in their first participation in the Yamazaki Nabisco Cup, advancing to the semifinals, with Yukihiko SATO winning the New Hero Award. Meanwhile, in the league, despite struggling toward the end, they finished in second place and secured promotion to J.League Division 1 (J1).

In 2000, the year FC Tokyo was promoted to J1, the team sparked the "Tokyo Whirlwind" by winning the first three matches of the 1st stage to finish 6th, and achieving five consecutive wins at the start of the 2nd stage to finish 8th (7th overall). The following year, 2001, saw the opening of their home ground, Tokyo Stadium (now Ajinomoto Stadium), and they won against Verdy in the inaugural match on March 10. They maintained a mid-table position with 9th in the 1st stage and 8th in the 2nd stage (8th overall), establishing a solid presence in J1 by their second year. After the season, Kiyoshi OKUMA, who had managed the team for seven years, stepped down, and Hiromi HARA took over as manager starting from the 2002 season. Building on the foundation of OKUMA’s "unyielding perseverance until the end" and "always giving full effort," the team entered a new stage under HARA’s leadership with a focus on "attacking soccer."

In 2002, the team struggled with injuries to key players and finished 10th in the 1st stage, but in the 2nd stage, thanks to the growth and performance of young players, they rose to 5th place (9th overall), gradually embracing Coach Hara's vision of attacking soccer. In 2003, with the abolition of extra time, the team adopted the slogan "90 minutes of attacking soccer," achieving their best-ever 4th place with the fewest goals conceded in the 1st stage, and in the following 2nd stage, they remained in the title race until the end, finishing 5th with the highest number of goals scored. Their overall ranking was also a record high at 4th place. After the season ended, Amaral, known as the "King of Tokyo" and a central figure of the team for 12 years, left the club, closing a chapter in the club's history.

In 2004, as the slogan "Aggressive, Dramatic, Attacking Soccer" indicated, the team adopted a more offensive stance than ever before. However, due to the dispatch of representative players for the German World Cup qualifiers and the Athens Olympics, the squad was not at full strength, and the J1 League finished 8th overall (6th in the 1st stage, 10th in the 2nd stage), which was far from a satisfactory result. Nevertheless, the team united and advanced to the final of the Yamazaki Nabisco Cup. Despite having a player sent off in the first half, they endured the full 120 minutes including extra time and won against the Urawa Reds in a penalty shootout. They secured the club’s long-awaited first title.

In 2005, the league changed to a single-stage system. With the slogan "Attack to take. Attack to win," the team held first place through the first four rounds but then suffered seven consecutive losses with one draw in between from the fifth round onward. Ultimately, they finished in 10th place, and after the season ended, it was announced that Manager Hiromi HARA, who had led the team for four years, would step down. In 2006, the club appointed its first foreign manager, Alessandro GALLO, and under the slogan "Ousadia – Trust, Courage, Challenge," they approached the season with a new style of play. However, amid a long break and an irregular schedule due to the Germany World Cup, the team's form did not improve, and GALLO was dismissed in August. From Sec. 18, Hisao KURAMATA, who had been the FC Tokyo U-18 manager, was entrusted with leading the top team, but with a six-game losing streak starting from Sec. 20 and other struggles, the team finished in a club-worst 13th place. Seeking a comeback in 2007, Hiromi HARA returned as manager with the slogan "It's Our Time – Blue Gale, Red Torrent." However, after losing the league opener, the team continued to struggle with losses piling up. New signing Wanchopé (former Costa Rica national team player) scored two goals by Sec. 11 but failed to produce the expected results and left the team by the end of June. Unable to find consistent momentum throughout the season, FC Tokyo finished 12th in the J1 League, concluding the 2007 season.