It spent the years 1994–2003 in the Victorian Premier League, winning the minor premiership twice, but was unable to secure the title during its time in the VPL.

The following year, Port were minor premiers in the VPL for the first time in their history, but successive losses in the finals series meant the season finished on a disappointing note.

Port Melbourne made an application to join the NSL ahead of the 1995/96 season[2] however this move was not approved and the club remained in the Victorian system.

In their first season back in the Victorian top-flight, the Sharks would have qualified for the finals had the league not been compromised by the Southern Stars FC scandal[5][6] and the club ended 2013 with a 6th-place finish.

In 2014, the first year of the National Premier Leagues system, Port Melbourne were seconds away from relegation until a 95th-minute goal from Conor Reddan in the final game of the season secured a draw against Werribee City, safety for the club and an 11th-place finish.

[9] In 2016, Port Melbourne were dealt three blows early on in the transfer window, with Kamal Ibrahim[10] and Nicholas Krousoratis[11] left for NPL rivals, but the club replaced them with the signings of Bonel Obradovic from Northcote City, David Stirton from South Melbourne[12] and welcomed back former player Lambros Honos, who rejoined the club he spent 2013 and 2014 with, after spending a season at Oakleigh Cannons.

[16] Following an 11th-place finish in 2017, the club parted ways with Barba[17] and appointed Adam Piddick who previously coached in the National Premier Leagues Queensland.