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The Club was founded in 1958 as Zillmere Stars Junior Soccer Club by a group of fathers, as Zillmere Church of Christ were unable to continue their teams. They played their games, and continue to play at O'Callaghan Park. There was a men's team at the time known as the Zillmere Magpies, but they had nothing to do with the new Junior club that had just started. In 1963 Zillmere Stars also started a Women's team. From the late 1970s, under the guidance of club president Laurie Anderson and director of senior football Jack Baron, the club rose from relative obscurity winning Division 3 in 1980, Division 2 in 1981 and became a dominant force in the late 1980s and early 1990s in the Brisbane Premier League. The club enjoyed outstanding success in junior and senior level football and, at one stage in the 1980s, was approached to join the National Soccer League (NSL). By the mid 1990s financial problems led to the club going amateur and suffering relegation. Re-founded in 1996 after combining business with Brisbane Strikers FC (currently in the NPL Queensland), the club were promoted to the Brisbane Premier League in 2011. Subsequent years have seen a return to the Brisbane Capital League 1. In 2016 they narrowly missed promotion back to the Brisbane Premier League by 1 point after being in first place with two rounds remaining. The club has a strong junior set-up. The senior men were promoted into the Brisbane Premier League 2020 after finishing 2nd in the 2019 season.

In 2018, North Star FC was granted a spot in the Women's Capital League 1 for the 2019 season with Kevin Gower as the inaugural coach. The women finished 4th in their first season.

2021 saw North Star FC handed a FQ license to be part of the newly formed FQLP2 competition. Gordon Tulley was brought on as the club's Technical Director. He brought Lee Cunningham on as Head Coach. The FQPL2 team finished 4th in their first season.