Pathan made his Test debut in the Second Test against Australia at the Adelaide Oval in December 2003. At the age of 19, he opened the bowling following an injury to the Baroda left-armer Zaheer Khan in a high scoring match. He took the wicket of Matthew Hayden while giving away 150 runs in a single game. He was dropped for the following Test upon the return of Zaheer, but was recalled for the Fourth Test at the Sydney Cricket Ground after Zaheer was reported being unfit. On another flat pitch, Pathan took the wickets of Steve Waugh, Adam Gilchrist and Ricky Ponting to claim 3/106. In the ODI tri-nation tournament against Australia and Zimbabwe that followed, Pathan was the leading wicket-taker with 16 wickets at an average of 31. In addition to two three-wicket hauls against Australia, he earned his first international man of the match award in the tournament, after taking 4/24 against Zimbabwe at the WACA Ground in Perth. However, his tour ended on a bad note after he was reprimanded by match referees for mocking the Australian batsman Damien Martyn after his dismissal in the second final.

Pathan subsequently led the pace attack again on the 2004 Test tour to Pakistan, taking 12 wickets and bowling a higher proportion of maiden overs than any other bowler to help secure India's first series victory over Pakistan in two decades. He also showed prowess with the bat, scoring 49 in the Second Test in Lahore after a batting collapse of the top order. He also took eight wickets at 17.8 in three ODIs, including three top-order wickets in the deciding fifth ODI in Lahore. His ability to swing the ball both ways and his innings in Lahore lead to speculation that he could become an all rounder. This saw him named as the ICC Emerging Player of the Year at its 2004 Awards ceremony. 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 with three three-wicket hauls. This continued during India's brief campaign at the 2004 ICC Champions Trophy, where he claimed 5 wickets at an average of 9