[3] In response, Football NSW made the decision to pull out its involvement with Sydney FC amid claims the A-League club had become a "plaything" for Frank Lowy and his family.

[8] Despite the unsuccessful attempt to establish a Western Sydney-based team in the form of Sydney Rovers (due to financial and technical reasons),[9] FFA were still strongly committed in pursuing a club in the region.

After a series of running battles between FFA and Clive Palmer – owner of Gold Coast United, over topics such as crowd control, stadium attendance capacities and breaches of A-League regulations.

[16] As notable Australian soccer players Scott Chipperfield, Tim Cahill and Lucas Neill expressed their support for the Western Sydney-based club,[17] so did the local soccer community, with FFA holding supporter forums in Mount Pritchard, Parramatta, Rooty Hill, Penrith, Castle Hill, Campbelltown and Bankstown, where community members discussed such topics as the club's values and culture, playing style, home ground, and proposed names and colours.

The squad was made up of relative unknowns, though included former Japan international and Asian Footballer of the Year Shinji Ono, as well as Jérome Polenz, Mateo Poljak, Youssouf Hersi, Iacopo La Rocca and Dino Kresinger.

[29] On 6 October 2012, Western Sydney Wanderers played their first competitive match of any kind against reigning A-League Premiers Central Coast Mariners in the first round of the league.

[39] Wanderers held second position behind Brisbane Roar throughout the majority of the season despite criticism over the team's squad rotation policy which Popovic implemented with consideration to the AFC Champions League and the short turnaround between matches.

Despite being down 3–1 on aggregate, the team managed to overturn the result and win 2–0 to progress to the quarter-finals in what was Ono's, Hersi's, Polenz's and inaugural captain Michael Beauchamp's final match for the club.

[50] The Cup loss was directly followed by Wanderers' continued campaign in the 2014 AFC Champions League; as due to the calendar format of the Asian tournament, the quarter-finals – a home and away series against Guangzhou Evergrande, resumed after a three-month break.

[53] In the return leg, Wanderers defeated FC Seoul 2–0, courtesy to goals from Mateo Poljak and Shannon Cole, which advanced the club to the 2014 AFC Champions League Final.

[56] Prior to the final match, Wanderers were criticised by the opposition coach in the media; after being crowned Asian champions, Tony Popovic responded by saying, "We were called a small club yesterday – today we are the biggest in Asia".

In the FFA Cup the Wanderers progressed with wins against Brisbane Roar & Palm Beach, then were beaten in a penalty shootout against Perth Glory in the quarter final.

In front of a sold-out crowd of 20,084 Brisbane started the game strongly by racing to a 3–0 lead inside 23 minutes but the Wanderers responded with two goals to make it 3–2 at half time.

Three days after the Sydney Derby they started their Asian Champions League campaign by losing 4–0 to Urawa Reds, and subsequent results saw them fail to qualify from the Group Stage.

On 19 April, after a disappointing season where the Wanderers failed to qualify for the 2017–18 A-League finals and players making problems with his management style known to reporters and the public, Gombau was fired.

It was reported in the media that Robinson had a release clause in his contract that allowed him to leave the Jets due to the dire financial situation of Newcastle whose owner Martin Lee had not funded the club since October 2019 and was stripped of his license.

[73] The Wanderers began the 2020–21 A-League season by releasing Radosław Majewski, Nicholas Suman, Mathieu Cordier, Nick Sullivan, Tristan Prendergast, Matthew Jurman and Mitchell Duke.

Several youth players were promoted, including Jarrod Carluccio and 16 year old Allesandro Lopane while German winger Nicolai Muller earned a contract extension.

The other teams had begun to catch up the number of games played and the Wanderers position on the ladder sank like a rock, falling to 9th place on 25 points, level with Wellington Phoenix but behind on goal difference.

With 5 minutes to play, Wanderers captain Marcelo was found unmarked from a free kick and a player of his quality should have scored but the ball went flying over the bar to groans from the crowd.

Layouni, who had started brightly in his short-term loan spell began talks with both the Wanderers and Melbourne City to join on a transfer but elected instead to return to a European club.

The Round of 32 away trip to Perth against Floreat Athena FC resulted in a 6–1 demolition of the NPL WA club, with Lachlan Brook scoring 5 goals, a cup record for a main stage fixture.

Rudan made headlines with a post-match tirade following multiple controversial officiating decisions, including 4 red cards in 3 matches and where Macarthur player Valère Germain scored a hat-trick when he should have been sent off early in the game for violent conduct and his winning goal awarded despite evidence showing it hadn't fully crossed the goal-line.

The second half of the season was a disaster, with a three-game horror run where Sydney FC beat the Wanderers 4–1 in Parramatta, followed that with a 3–1 loss to last placed Western United & an away game against Melbourne City four days later ending in a 7–0 club record defeat where Terry Antonis, who had been frozen out & forced to leave by Rudan scored the goal of the season with a lob over Lawrence Thomas from the half-way line for the final goal.

[85][86] The post-season player clear out saw the departures of Daniel Margush, Sonny Kittel, Valentino Yuel, Doni Grdic, Marcelo, Jorrit Hendrix, Lachlan Brook and Jack Gibson due to injury.

[93][94] In September 2015, the club announced the formation of a formal partnership with Blacktown City Council that made the Sportspark the long-term training and administrative home of the Wanderers.

[118] On 19 April 2013 Australian rock-pop band Exit Row (Andrew Torrisi, Nick Ferreri, Raf Lavorato, Jeremy Azzopardi and Aaron Tarasiewicz) released their debut single "Welcome To Our Wanderland",[119] a Western Sydney Wanderers-anthem.

[120] By the end of their inaugural season Western Sydney Wanderers had grown its membership base to 7,500 people,[121] with the club's total match attendance at home reaching 174,520, with an average of 12,466.

[125] Some notable Wanderers fans include Ian "Dicko" Dickson,[126][127][128] Laura Dundovic,[129][130] Nicole da Silva,[131][132] Lucy Zelic,[133][134][135] Paul Croft,[136] Montaigne,[137] and Jamie Soward.

[148][149][150] The two clubs first met in the opening round of the 2020–21 A-League season on 30 December 2020, with Macarthur winning the match 1–0 after a goal scored by Mark Milligan in front of a crowd of 10,128.