The club's founders were president Yan Skwara and Vice-president/general manager Sam Kaloustian, and during the A-league years its head coaches included Ralf Wilhelms, Costa Skouras, Papo Santos, and Colin Clarke.

[3] The Flash were fairly successful during their short stint in the league, winning the Pacific Division in 1998 and 1999, finishing second in 2000 and 2001, progressing to the quarter-finals of the A-League playoffs in 2001, and reaching the third round of the US Open Cup on two separate occasions.

The club was resurrected in 2010 by a new ownership group, the San Diego Soccer Partners, Inc., which is headed by former Flash part owner Clenton A. Alexander, former English Premier League footballer and Fox Soccer Channel analyst Warren Barton, former US national team striker Eric Wynalda, and former San Diego Boca FC General Manager Travis Chesney.

The move from their exhibition location in downtown San Diego was the decision of Flash Soccer CEO; Clent Alexander, for the team to play in a more modern facility.

[4] The 2012 season did start on a somewhat sour note for the Flash having been eliminated from the US Open Cup by their crosstown rival San Diego Boca FC.

Near the end of the season the team itself enjoyed its two largest home crowds to that point and also began exploring the possibility of moving to the Division 2 North American Soccer League with Alexander presenting a letter to and meeting with the NASL.

[5] The team did suffer from a second consecutive early exit from the playoffs in the divisional semi-final losing to the Sonoma County Sol on penalty kicks 5–3 after the game ending in a 2–2 draw.