Although Pathan's batting continued to be productive, he was not regarded as a specialist and was dropped from the team in both Tests and ODIs by the end of 2006, and by 2007 was no longer in the squad until his return in the 2007 World Twenty20.

Irfan Pathan, along with players such as Vinod Kambli and Laxman Sivaramakrishnan, was included in the list of "India's lost boys" by Shashi Tharoor.

For the first nine months of Chappell's stint at the helm, Pathan performed strongly with both bat and ball, scoring runs regularly and frequently taking top-order wickets.

This earned him a recall into the ODI team, where he was a regular for most of the next 12 months before being dropped as his economy rate continued to trend upwards and subsequently struggled with a loss of form and injuries.

In the beginning his deliveries did not reach the other end of the cricket pitch, but rigorous six-hour training sessions in blazing heat and his family's sense of discipline saw him progress steadily.

[17] In late 2003, he was selected for the India Under-19 team to compete in an Asian youth ODI competition in Pakistan, where he was the leading bowler with 18 wickets at 7.38, with an economy rate of 3.54.

After stand-in captain Rahul Dravid enforced the follow on, Pathan tied the Pakistanis down, bowling 12 maidens in his 21 overs to end with 2/26 as India secured an innings win.

[33] Pathan continued his productive form in ODIs at the 2004 Asian Cup in Sri Lanka, where he was the leading wicket-taker with 14 wickets at 16.28 at an economy rate of 4.37 in six matches, with three three-wicket hauls against the United Arab Emirates, Bangladesh and Pakistan respectively.

[39] Pathan was subsequently signed by Middlesex County Cricket Club for the English country season, where he attempted to regain his form after his bad start to the year.

[17] He showed further signs of returning to peak form in the Videocon Triangular Series in Zimbabwe, taking 10 wickets at 16.10 at an economy rate of 5.03 and scored 60 runs at 30.00 in four matches.

In the following match in Ahmedabad, he scored 82 runs and combined in a century stand with V. V. S. Laxman to revive India after an early batting collapse saw five wickets fall during the first half of the opening day.

After not getting an opportunity in the First Test—India lost only one wicket—Pathan made use of the good batting conditions himself and scored 90 in a double century partnership with wicket-keeper Mahendra Singh Dhoni in Faisalabad.

[46][47] It was also the highest in terms of total averages of the batsmen dismissed (130.18: Salman Butt 34.27, Younis Khan 46.04, Mohammad Yousuf 49.86) and came after 1783 Tests in the history of cricket.

He finished with a haul of 5/61 after the hosts staged a lower-order counter-attack but was punished in the second innings, taking 1 wicket while conceding 106 runs as Pakistan set a target which was beyond India's reach.

[17] Pathan began to suffer a loss of form during the tour of the West Indies in May 2006, when he managed only 24 runs at 6.00 and took 6 wickets at 29.83 at an economy rate of 5.59 while bowling in the ODI arena as India lost the series 4–1.

[17] Pathan was then demoted from the position of an opening bowler in ODIs during the 2006 ICC Champions Trophy; he took four wickets at 24.00 at an economy rate of 4.80, and scored only 29 runs at 9.66,[17] as India were knocked out in the first round.

Despite this, Indian captain Rahul Dravid remained optimistic about Pathan's prospects, stating "The number of Man-of-the-Matches that Irfan has won is a testimony to the fact that he's a proven matchwinner for us.

[54][55] He subsequently led Baroda to the semi-finals after scoring 82* to help defeat Uttar Pradesh by five wickets, but his bowling remained ineffective, returning figures of 2/108 and 1/59, conceding 4.77 runs per over.

Pathan was initially dropped for the ODI series hosted by India against the West Indies, but was recalled for the final match in his home town after claiming seven wickets against Mumbai in the Ranji Trophy semi-final.

[27][58] The selectors persisted and named him in the squad for the 2007 Cricket World Cup,[59] but injury stopped him from playing in the ODI series against Sri Lanka, denying him an opportunity to regain form.

[67] As a result of his performances in South Africa, Pathan was recalled to the ODI team and played in the home series against Australia and Pakistan in late 2007.

Pathan scored his maiden Test century, reaching the mark with a six from leg spinner Danish Kaneria to move from 96 to 102 with only last man, paceman Ishant Sharma left to accompany him, before holing out in the same over.

Pathan held his place in the ODI team and played all 10 matches in the Commonwealth Bank Trophy, scoring 118 runs at 19.66 mostly in the lower order and taking 11 wickets at 34.27 at an economy rate of 5.49.

[27] His top-score of 31 in the series came in partnership with captain Mahendra Singh Dhoni in the closing stages of a successful and tense run-chase against Sri Lanka.

[17] Pathan returned to India and took 3/50 and scored 51 not out in his only domestic one-dayer for Baroda during the season, which ended in a win, before leaving for the limited overs leg of a tour to New Zealand.

[17] He then played in all 14 of Punjab's round-robin matches in the 2009 Indian Premier League held in South Africa, taking 17 wickets at 22.94 with an economy rate of 7.74, and scored 196 runs at 19.60.

[17] Since then, Pathan was dropped from the limited overs team and was then injured for an extended period, until he made his return to cricket in the Ranji Trophy in November.

In his most productive first-class season with the bat, Pathan made starts in eight of his nine innings, only failing to reach 24 once, and scoring four fifties, although he was unable to convert any to triple figures.

Furthermore, on 25 February 2010 the Board of Control for Cricket in India (BCCI) announced its list of 30 probables for the T20 World Cup to be held in the West Indies, the most notable omission being Irfan Pathan.

[81] BCCI announced on 13 July 2012 inclusion of Irfan Pathan in the Indian team for the tour of Sri Lanka as a replacement to the injured Vinay Kumar.