After a breakout season for the Brumbies in 2012, he was signed by the New South Wales Waratahs for the 2013 season. 2012 had been a standout year for Hooper who won numerous accolades including Best Forward (for the Brumbies), the ARU's Rookie of Year and placing third for the John Eales Medal after playing less than half of the polling games.

In 2013, Hooper played every Waratahs Super Rugby game of the season and he won the Australian Super 15 Player of the Year award, as well as the Waratahs' Player of the Year award.

on the 1st of March 2014, Hooper was named captain for the Waratahs' clash with the Queensland Reds after team regular Dave Dennis was ruled out due to injury received in the Waratahs' first game of 2014 against the Western Force. Hooper led the Waratahs to a 32–5 win over the Reds at ANZ Stadium and went on to play all the remaining games of the 2014 season including the Grand Final against the Crusaders in which he captained the side to a 33–32 win at ANZ Stadium. It was the franchise's maiden Super Rugby title.

In August 2020 it was announced that Hooper had signed to play for the Japanese Top League club Toyota Verblitz for the 2020–21 season,[9] marking his first serious move to play domestic rugby outside the Super Rugby since starting his career with the Brumbies in 2010.

On 5 June 2012, Hooper made his international debut for Australia, coming off the bench (in the 65th minute) against Scotland in Newcastle. Following a knee injury to regular flanker and captain David Pocock, Hooper started in every Test game until the final Spring-Tour game (and Nathan Sharpe's final Wallabies game) against Wales in Cardiff, where he started from the bench to make-way for David Pocock. Hooper won Wallabies 'Rookie of the year' award at the annual John Eales Medal awards evening event.

In 2013, when David Pocock suffered a season-ending knee injury; Hooper played in all of the Wallabies Test matches and had an outstanding year, winning the John Eales Medal as 'Wallabies player of the year'.

In 2014, Pocock suffered another season-ending knee injury and in Ewen McKenzie's second year as Wallabies coach, McKenzie named Hooper as vice-captain with his Waratahs team-mate Adam Ashley-Cooper and his former Brumbies team-mate Stephen Moore was named as Australia captain for the 2014 three-test June series against France. However, when captain Stephen Moore left the field with a knee injury in the 5th minute, Hooper took over the captaincy for the rest of the game. During the game, he scored a try in the first half and he had a strong performance against France in the Wallabies' 50–23 win at Suncorp Stadium. Hooper was rated was one of the best players on the field during the game by Iain Payten of foxsports.com.au and was also labelled 'the Energizer Bunny of world rugby'.

Following the season-ending injury to Stephen Moore during the first test of 2014 against France in Brisbane, Hooper was named as Wallabies captain for the rest of the 2014 Test-season, meaning that he was the Wallabies 82nd Test captain and the youngest player (age 23, 233 days) to captain the side since Ken Catchpole (age 21, 354 days) in 1961.

Following another strong 2015 Super Rugby season, Hooper was awarded the Peoples Choice – Wallaby of the Year at the John Eales Medal awards night for the second year in a row.[19] He also kept his starting position safe, forcing David Pocock into Number 8 after returning from injury. He was also selected in the 31-man 2015 Rugby World Cup squad.

In 2016, Hooper was again awarded the John Eales Medal, the 4th player to have won it a second time.

Hooper became the full-time Wallabies captain for the 2017 Rugby Championship, following Stephen Moore announcing that the 2017 season would be his final year of test rugby.

His very rough playing style has led Hooper to collect nine yellow cards in his international career, matched in this unenviable record only by the Georgian Viktor Kolelishvili.

In 2020, Hooper played his 100th test for Australia, becoming the fastest Wallaby to reach 100 tests. He also became the youngest-ever player to reach 100 tests for his country, although his record was later broken by Wales' centre, George North.[citation needed] Hooper's 100th test was a 16–16 draw with New Zealand, at the Wellington Regional Stadium. He went on to play all 6 of Australia's tests in 2020, under the new Head Coach, Dave Rennie.

In 2021, Hooper surpassed George Gregan's record for the most caps as Wallabies captain, 60.

In August 2023, Hooper was omitted from the Australian squad for the 2023 Rugby World Cup. At that time, Hooper was the fastest player to 50 caps and longest serving Wallabies captain[24] Wallabies coach Eddie Jones cited Hooper's calf injury as a reason for his omission.

On the 30th of June 2024, Hooper announced his retirement from Australian rugby and his Olympic Rugby 7s bid.

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