Younus made his international debut in an ODI against Sri Lanka at Karachi in February 2000, and has since played over 150 ODIs for Pakistan. He has also played 54 Tests. Younus was one of the few batsmen who retained his place in the team after Pakistan's disastrous World Cup campaign in 2003, but lost it soon after due to a string of poor scores in the home series against Bangladesh and South Africa. He came back for the one-day series against India, but failed to cement a place in the Test side.

It was his return to the side in October 2004, at the pivotal one-down, against Sri Lanka in Karachi that laid the groundwork for his emergence as a force in Pakistan cricket. He was the top run-getter in the disastrous 3-0 whitewash in Australia