In 1997 the Seals was called the "Team of the Year" by USA today after beating the Seattle Sounders, the Kansas City Wiz (now Sporting), and the San Jose Clash (now Earthquakes) in the Lamar Hunt U.S. Open Cup.

Drawing on talented players from throughout the Bay Area, SFUSC soon became a "super club" and a dominant force in California state youth soccer.

In 1993 the New Zealand All Blacks sent a cease and desist letter claiming copyright infringement forcing the team to change their name to the San Francisco Bay Seals.

Then, in 2006, after a six-year gap, the original club owners resurrected the senior team, this time as a franchise in the PDL as the San Francisco Seals.

Their first year back in competition was fairly decent – four wins in their first six games, including a comprehensive 3–1 over California Gold – left the team well in contention for the playoffs as the second half of the campaign began.

However, a disappointing run of results in the latter half of 2007, including a winless streak of 5 games from mid-June to early July saw the team slip down the table, eventually finishing 6th.

Jose Diaz and Peruvian striker John Colan were the team's top scorers, notching 13 goals between them, while Shani Simpson contributed 4 assists.

The Seals eventually finished a comfortable mid-table 6th; Anton Peterlin and Keith Ratzburg were joint top scorers with 3 goals each, while Richard Halvorsen registered 3 assists.

In December 2008 the Seals announced that, due to the folding of their local competition, the San Jose Frogs, and the state of the economy, they would not be fielding a PDL team in 2009.