On February 12, 1989, the WSL and ASL announced they were working toward a merger. The first sign of their partnership would be the ASL-WSL National Championship Game played at Spartan Stadium in San Jose, California. Fort Lauderdale (ASL) defeated San Diego (WSL) in the National Final, which was telecast to 10 million cable households nationwide.

With their initial venture a success, the two leagues announced on February 22, 1990 that they had merged under the American Professional Soccer League banner for business and marketing purposes. Six weeks later, the leagues opened their first season as partners playing as independent conferences with a national championship.

The ASL opened with just one expansion team, Penn-Jersey Spirit, while the WSL would add the Colorado Foxes, Salt Lake Sting and New Mexico Chiles. In the first official APSL Championship Game Maryland and San Francisco Bay staged a memorable struggle in the rain in Boston before a national cable audience with the Bays edging the Blackhawks on penalty kicks after a 1-1 tie for the first APSL title.

In 1991, the two conference runners-up from the regular season met up in the final with the Blackhawks winning the title over the Albany Capitals. The Blackhawks won the second game of the two-leg series, forcing the mini-game tiebreaker, which would end on penalty kicks.

The 1992 APSL Championship game showcased two first-time finalists, the regular season champion Colorado Foxes and runners-up Tampa Bay Rowdies. Reverting back to the single-game, winner-take-all format, the Foxes shaded the Rowdies 1-0 on a brilliant first half free kick by midfielder Chad Ashton.

In 1993 the APSL expanded north of the border to Canada with the addition of the Montreal Impact, Vancouver 86ers and Toronto Blizzard. It was the second straight season the Foxes would claim the title, becoming the first franchise in the history of the APSL and its predecessors to win back-to-back championships. The Foxes came back from a 1-0 deficit with three minutes left and went on to defeat the LA Salsa 3-1 with two goals in overtime.

Montreal became the first Canadian team to win the APSL Championship in 1994 with a 1-0 victory over two-time defending champion Colorado. Both teams reached the final after finishing third and fourth in the regular season, respectively. The third-seeded Montreal Impact defeated Los Angeles on penalty kicks in the mini-game tiebreaker and the Colorado did the same versus the expansion Seattle Sounders, who won the regular season championship in their inaugural campaign.

Following their fifth successful season in 1994, the league altered its name, to reflect its Division II status, to A-League. The Impact and Sounders were again at the top in 1995. Regular season champion Montreal, however, fell to the expansion Atlanta Ruckus in the semifinals via a shootout in the three-game series finale, while regular season runners-up Seattle defeated the Vancouver 86ers two games to one.
Seattle fell behind to Atlanta, losing the shootout in Game One of the three-game championship series. The Sounders rebounded with a 3-0 hammering of Atlanta in Game Two and captured their first title with a 2-1 shootout victory in Game Three.

The Colorado Foxes returned to form in 1996, finishing second to Montreal in the regular season. The Sounders, however, won their second consecutive championship by defeating Colorado two games to one in the semifinals, and the expansion Rochester Raging Rhinos 2-0 in the 1999 championship match.

The rookie Rochester Raging Rhinos made history of another note in the US Open Cup, becoming the first A-League team to reach the Open Cup Final. The Raging Rhinos knocked off the Tampa Bay Mutiny 4-3 and the Colorado Rapids 3-0 of the first-year Major League Soccer before losing 3-0 to DC United, who also went on to capture the MLS crown.