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The club is San Diego's first women's professional soccer team since 2003, when the Women's United Soccer Association folded and forced the San Diego Spirit to disband.

In January 2021, Lisa Baird, the commissioner of the National Women's Soccer League (NWSL), announced that an expansion team in Sacramento, led by Ron Burkle and in conjunction with Sacramento Republic FC's expansion bid into Major League Soccer, would join the NWSL in 2022. However, Burkle never confirmed the news publicly before exiting the Sacramento Republic's ownership group. Instead, on June 8, 2021, the NWSL announced San Diego as the location for an expansion team owned by Burkle to begin play in 2022. On November 9, it was announced the club would be called Wave Fútbol Club.

2022 (inaugural season)

San Diego Wave FC officially began play on March 19, 2022, in the NWSL Challenge Cup against fellow expansion team Angel City FC on the road, where they drew 1-1. They were eliminated from the Challenge Cup after finishing third in their group. The club began their inaugural season on May 1 and opened with three straight wins, sitting on the top of the table for over half the season before finally falling to the KC Current 2–1. Although briefly gaining the top spot twice late in the season, Wave FC finished 3rd and qualified for the quarter-finals of the playoffs. After defeating the Chicago Red Stars 2–1, the club traveled to Providence Park to play against the Portland Thorns in the semi-finals, losing 2-1 following a Crystal Dunn goal in the final minutes of the game.

2023

In the 2023 season, Wave FC continued their winning ways, slightly improving upon their record in 2022 and securing the NWSL Shield with two games to spare after beating the Portland Thorns on September 30 and guaranteeing a bye for the playoffs. Wave FC faced OL Reign in the semi-finals, losing 1-0 after Veronica Latsko scored in the 47th minute, marking the second year in a row Wave FC were eliminated in the semis. Defender Naomi Girma was named U.S. Soccer's Female Player of the Year, recognizing her excellence for Wave FC and for the U.S. Women's National Team.

2024

In the 2024 NWSL Draft, Wave FC selected Kennedy Wesley with the 12th pick in the first round and Mya Jones with the 42nd pick in the third round. Wave FC had traded away their natural 26th round pick in the second round, 40th pick in the third round, and 54th pick in the fourth round.

On March 14, it was announced Wave FC would be sold in a deal that places the club's value at $113 million, a record outlay for an NWSL club.

On March 15, Wave FC won the Challenge Cup 1-0 over 2023 champion NJ/NY Gotham FC thanks to an 88th minute goal from Alex Morgan.

On March 22, one day before their regular season opener, Wave FC announced they had signed 16-year-old midfielder Kimmi Ascanio through the NWSL's Under-18 Entry Mechanism.

On March 23, Wave FC set the current record for NWSL season home opener attendance with 32,066 fans attending their 2-1 loss to the Kansas City Current.