While NZS was given a chance to apply with a new sub-licensee, a Townsville-based consortium, Tropical Football Australia (TFA) also expressed interest and prepared an A-League application to replace the place previously held by the Knights.

After much delay, the final amount needed for the application came from Wellington property businessman Terry Serepisos in the latter stages of the bid.

[6][7] Serepisos said of the name, that "It symbolises the fresh start, the rising from the ashes, and the incredible Wellington support that has come out".

[10] In the 2009–10 season, Wellington Phoenix became the first New Zealand side to reach the playoffs of an Australian football competition when Adelaide United beat Brisbane Roar 2–0 in the 26th round.

The loss brought the end to the Phoenix's season, meaning that Melbourne Victory and Sydney FC would compete in the Grand Final.

On 20 April 2010, FFA granted Wellington Phoenix a five-year licence extension, keeping it in the competition until at least the conclusion of the 2015–16 season.

[11] Many argue Wellington's ability to play in the A-League as being instrumental to the progress of the New Zealand national side and the wider football landscape.

Additional stories also emerged that coach Ricki Herbert was personally owed $100,000 in unpaid wages by the club.

[14][15][16] On 26 February 2013, with the Phoenix sitting in last place, Ricki Herbert resigned from the position of head coach.

[24] On 30 May 2018, Wellington Phoenix announced the appointment of former Sydney FC captain Marko Rudan as manager on a two-year contract.

[28] After a defeat in Round 5 against Adelaide United, Phoenix went on a 9-game undefeated streak including draws with Premiers Perth Glory and Champions Melbourne Victory, and wins over clubs like Sydney FC and Newcastle Jets.

[31] On 4 May 2019, it was announced Ufuk Talay would be taking the reins of head coach after the departure of Marko Rudan on a one-year deal.

[32] In his first press conference, Talay expressed his idea of building a young team with a strong Kiwi core.

[38] On 24 July, it was announced that Steven Taylor would be the captain heading into the new season[39] while Alex Rufer was made vice-captain.

[41] Talay also made a handful of signings of young Australian players including Walter Scott,[42] Jaushua Sotirio,[43] Cameron Devlin,[44] Liam McGing,[45] and experienced centre-back Luke DeVere.

[47] Talay had a positive start to his managerial tenure with the Wellington Phoenix when he led them to a 7–0 victory over Wairarapa United in a pre-season friendly in his first match in charge.

[48] They were knocked-out of the 2019 FFA Cup in the Round of 32, losing 4–2 on penalties to Brisbane Strikers, after making an extraordinary comeback from 2–0 down to a 2–2 draw at full time.

[49] On 22 May 2021, Wellington Phoenix broke their home attendance record, attracting 24,105 spectators against Western United FC.

[50] On April 14, 2023, Talay announced that he would be leaving the club at the conclusion of his fourth season in charge citing ambitions to coach outside of the A-Leagues.

[53] When Reebok lifted constraints on kit designs in 2009, Phoenix adopted yellow and black vertical stripes.

The updated badge also featured the club's new motto of 'E Rere Te Keo',[56] a rising call rooted in the Māori legend of Taniwha.

[59] The NZD$130 million stadium was built in 1999 by Fletcher Construction and is situated close to major transport facilities (such as Wellington railway station) one kilometre north of the central business district.

The Phoenix previously trained at Newtown Park, on a ground that was specially redeveloped in 2008 and separate to the playing pitch.

This ground was shared with NZFC franchise, Team Wellington however in 2017 the Phoenix moved to Martin Luckie Park which had been redeveloped with two full-sized sand-based pitches.

[62] Due to COVID-19 in both New Zealand and Australia, the Wellington Phoenix-based themselves in Wollongong and played home games at WIN Stadium for the 2020–21 A-League season.

The main supporters' group, named the Yellow Fever, was founded a day after the Wellington Phoenix's formation was announced.

The Yellow Fever are renowned within the A-League for their traditions; the most prominent of which being if the Phoenix are winning by the 80th minute, members remove their shirts.

The former official podcast of Yellow Fever, 'Phoenix City', is hosted by Patrick Barnes, and features Cameron McIntosh and Andrew French as panellists.

[72] Although the initiative only lasted four seasons, the scholarship is widely credited with bringing New Zealand international Marco Rojas professional attention.

During the 2021/22 season Macarthur FC won the Australia Cup, with Western United winning the 2022 A-League Men Grand Final.