Though his form in ODIs was strong, bolstering Australia's middle order, a knee injury in the 2009 ICC Champions Trophy final took him out of competitive cricket for 11 months and he lost his place in the national side.

[10] Ferguson scored a duck in a disastrous yet memorable innings for South Australia in which they were dismantled for a record low total of 29, mainly due to a devastating spell of 7/4 from Australian representative Nathan Bracken.

[14] Ferguson's second season also saw him produce solid results, as he scored 506 first-class runs at an average of 36.14[15] and was one of 15 players to be selected for the Australian Cricket Academy.

[18][19] This resulted in him being dropped from the South Australian side in December before being recalled in late February,[20] when he scored a match-winning half century in a one-day match against Tasmania.

[24] For the 2008 winter, Ferguson went to northern England to play for Netherfield Cricket Club after being told by his state coaches that he needed to convert his starts into larger scores more often.

[29] Ferguson scored totals of 81 and 115 in a Sheffield Shield match against Victoria, and five minutes after his second dismissal he learned that he would be brought into the national team's 13-man squad for the second and third ODIs against New Zealand due to the absence of captain Ricky Ponting and an injury to Shaun Marsh.

[26] He made his One Day International debut, his first match representing Australia, against New Zealand at the Melbourne Cricket Ground on 6 February 2009.

[33] In the second match he scored another ODI half-century, resurrecting the Australian innings after they'd collapsed to 5 for 19, though his work wasn't enough to get Australia the win.

Chairman of selectors Andrew Hilditch described cutting Ferguson as "the hardest selection of them all," saying "He is a young kid who has taken all the opportunities that have come his way and done exceptionally well.

[38][39] In this series he had the best ODI innings of his career, surviving through difficult bowling spells to score 71 not out at The Oval against England and being awarded the man of the match, with Australian captain Michael Clarke noting the "beauty" of his batting.

[40] He was one of the key players for Australia in the series win against England, scoring two half-centuries and twice being at the crease to seal run chases.

[41][42] Ferguson was part of Australia's 2009 ICC Champions Trophy-winning squad in South Africa,[43] which he described as the "hugest" event of his career so far.

He would have been prepared to bat in Australia's run chase if needed,[45] though later tests revealed that he would require a knee reconstruction, taking out of competitive cricket for at least six months.

[47] Ferguson came back from injury to be named in Australia's squad for their ODI series in India in October 2010,[48] but persistent rain meant he was unable to play any matches[49] and he was then left out of Australia's squad for the next ODI series against Sri Lanka until a back injury forced Shaun Marsh out of the team.

[50] Ferguson made his first-class return from his injury in the 2010–11 Sheffield Shield season with a century in Brisbane, putting his name up to potentially play in the 2010–11 Ashes[51] and earning a place in an Australia A squad for a tour match against England,[52] but he didn't impress national selectors with scores of 7 and 10.

[53][54] Though he was included in a large 17-man squad for the first Ashes test,[55] his poor form in the Australia A match meant he failed to earn his baggy green.

[60] Ferguson came into the side in the second ODI to replace the out-of-form Cameron White but was not required to bat as Australia only lost one wicket in their innings.

[63] Ferguson signed up for the 2011 Indian Premier League player auction, where he was bought by the Pune Warriors India for $300,000,[64] though he missed the start of the tournament as he was still with the Australian side in Bangladesh at the time.

[69] Since his brief ODI career, Ferguson has consistently performed well enough in domestic cricket to be in contention to play for Australia, but has struggled to actually break into the Australian side.

[82] In the next match against New South Wales he hit ten fours and two sixes to put on 80 and was part of a 148-run partnership with Phillip Hughes.

[85] His best performance for the side came in the final match against South Africa A, where he scored 82 runs as part of a 182-run partnership with Phillip Hughes.

[86] Ferguson had to fight hard for runs in the 2014–15 Matador BBQs One-Day Cup as South Australia had a poor tournament and finished as the bottom-placed team.

[87] Ferguson started the Sheffield Shield with an unbeaten century against Queensland, finishing on exactly 100 not out when the Redbacks declared in the first innings on their way to an eight-wicket win.

[96] When the Sheffield Shield resumed, Ferguson fell short of a century twice in the same match against Western Australia, with scores of 81 and 84 in a loss.

He then began the 2015–16 season in great form, scoring three centuries with only one dismissal in the West End Premier League to achieve an average of 405.

[105] Unfortunately for Ferguson, when he was training with the Melbourne Renegades in December, he suffered a serious knee injury for the third time in his career, prematurely ending his season.

[104] Ferguson returned from his knee injury over the off-season and, in his first match back in competitive cricket, he scored 122 in the Premier League.

His replacement was the younger Nic Maddinson, who had a less consistent and less successful first-class record than Ferguson, and former Australian Test cricketers Brett Lee and Michael Hussey both said that he had been unlucky to be dropped after having just one opportunity.

[121] Ferguson was again named as the captain of the Redbacks’ 14-man squad for the 2017–18 JLT One-Day Cup in the absence of Travis Head, who was playing for Australia in India at the time.