Having made his List A debut for Quetta in the 1998/99 Tissot Cup against Hyderabad, a tournament in which he made five appearances for the team,[2] Khan made his first-class debut for Pakistan Customs against Lahore City in the 1999/00 Quaid-e-Azam Trophy.[3] In that same season he also made his List A debut for Pakistan Customs against Karachi Whites in the 1999/00 Tissot Cup.[2] Khan made a total of 30 first-class appearances for the team between the 1999/00 and 2004/05 seasons,[3] scoring a total of 1,430 runs at an average of 36.66, with a highest score of 127.[4] This score, which was one of two first-class centuries he made for the team, came against the Water and Power Development Authority in 1999.[5] Over the same period, he represented Pakistan Customs in 26 List A matches,[2] scoring a total of 1,148 runs at an average of 44.15, with a highest score of 123.[6]
This score was one of three centuries he made in that format for Pakistan Customs and came against the Water and Power Development Authority in the 2001/02 Departments One-Day Tournament.[7] During his period playing for Pakistan Customs, Khan also played county cricket in England for Cambridgeshire, making a single List A appearance for the Minor county in the 2nd round of the 2003 Cheltenham & Gloucester Trophy against the Middlesex Cricket Board, which was held in 2002 to avoid fixture congestion the following season.[2] He didn't appear in Minor counties cricket for the county. He also continued to make List A appearances for Quetta during this period, making a total of eleven appearances up to the 2003/04 season.[2] He scored a total of 377 runs at an average of 41.88, with a highest score of 101 not out.[6]
He also made his first-class debut for Quetta during this period, against Multan in the 2003/04 Quaid-e-Azam Trophy. To date he has made 46 first-class appearances for his home city,[3] scoring 2,417 runs at an average of 30.21, with a high score of 151.[2] He has also represented the Quetta Bears in limited-overs cricket, making his List A debut for the team against the Multan Tigers in the 2004/05 ABN-AMRO Cup. To date he has made 21 List A appearances for the team,[6] scoring 562 runs at an average of 26.76, with a highest score of 62.[6] It was for the Quetta Bears that he made his Twenty20 debut for against the Rawalpindi Rams in the 2004/05 ABN-AMRO Twenty-20 Cup. He made eleven Twenty20 appearances for the team between the 2004/05 and 2007/08 seasons, with his final appearance in that format coming against the Rawalpindi Rams in the 2007/08 RBS Twenty-20 Cup.[8] In his eleven appearances, he scored a total of 154 runs at an average of 14.00, with a high score of 32.[9] In the 2007/08 season, he made his debut for Baluchistan in a first-class match against Federal Areas in the 2007/08 Pentangular Cup. He played for Baluchistan in the 2007/08 and 2008/09 competitions, making five appearances[3] and scoring a total of 122 runs at an average of 12.20, with a high score of 38.[4] Khan has also appeared eight times in first-class cricket for the Rest of Baluchistan,[3] scoring a total of 471 runs at an average of 31.40, with a highest score of 104.[4]