In 1997, the Albion Redsox were forced into move away from Selwyn Park after a dispute with the Council in the sharing of the facilities at Selwyn Park. Limited opportunities in finding a new home meant the club would take an offer from the Melton Shire Council to base itself out of McPherson Park in Melton, Victoria. The move, which was approximately 25 km away from its current base, would include a name change as the club would be known as the Melton Reds. The relocation seemed viable at the time but a significant decline in the club's supporter base and revenues would prove detrimental to the club. The Reds were relegated from the VPL after a disappointing year however the club would continue the suffering with back to back relegation in 1998.
In 1999, the Albion Reds Soccer club decided to change its name to be known as the Satellite City Rovers in a bid to attract new interest to the club. The change lasted until the end following season where the club continued its struggle to survive. As a result, in 2001 the club ended its lease early with Melton Shire council and temporarily relocated back closer to its original home of Selwyn Park. The temporary move would see the club base themselves at the home of the Sunshine George Cross Soccer club in Sunshine, Victoria as the Rovers continued to struggle in finding a new base close to its original home of Selywn Park. The club eventually relocated to the Calabria club in Uniting Lane, Bulla, Victoria where facilities including a car park, clubroom and reception center were available. It was probably another key decision to see the return of the Albion Rovers Soccer club name that attracted some of the club's loyal supporter base to return. The 2001 season ended in success as the club went on to be crowned champions of Victorian State League Division 2 North West.
In 2003, the club would begin another turbulent period in the its history. A change of ownership and lack of support resulted in the Rovers being relegated to below division, however the suffering would continue with back to back relegation in 2004. While the Soccer club was to stabilise in the following season, underlying problems remained with a lack of support and finances, so another move was decided by the club owners. The Rovers relocated to temporarily base themselves out of Green Gully Reserve in 2006, where the club's juniors were based, while negotiations took place on a potential new permanent home. The 2006 season would see the club miss out on promotion by a single point.
It was in 2007, after much negotiation and assistance from the Brimbank City Council and in particular Mayor Natalie Suleyman, the Soccer club would be awarded brand new facilities at the home of Kevin Flint Reserve in Cairnlea. The new home would feature two football grounds with extensive lighting, a large clubroom, 4 change rooms and large car park. The move included formally changing the club's name to Cairnlea FC. The move also reinvigorated the club and its members, and season 2007 saw the club achieve promotion after finishing second in the Victorian State League Division 3 North West. The success was short lived and the step up proved a difficult task for the club as a second bottom finish resulted in relegation from Victorian State League Division 2 North West in 2008.
However, it was during this time Cairnlea FC decided to invest on its up-and-coming Senior Girls' football team. The girls begun to emerge as a powerhouse of female football in the western suburbs of Melbourne. In remarkable fashion, the Senior Girls' would go on a run of back to back promotion in years 2009, 2010 and 2011. The success paved the way for the Girls' team to compete in the Victorian Women's Premier League – the highest possible state league for woman. The club's girls' team were able to backed up their impressive performances by winning the annual Brimbank Cup in years 2012, 2013 and 2014.
In 2013, the club added another promotion by finishing champions of Victorian State League Division 3 North West in remarkable fashion. The season included a 10-game unbeaten run that ended on the final day of the season where Cairnlea FC would travel away from home requiring one point to finish first. This was the first time in Cairnlea FC history, and only the second time since its amalgamation with the Albion Rovers Soccer Club that it had won a championship.