He started his career as a left arm seamer with the 2nd Division side, Bangladesh Sporting, in 1985. In 1988, he joined Bangladesh Biman cricket team. There, under the influence of the Pakistani allrounder Wasim Haider he converted to slow orthodox spin bowling.
In December 1994 he played for the Bangladesh team in the 2nd SAARC cricket tournament where he had a 3/25 in the Bangladesh win against India "A".
He was a member of the Bangladesh team that won the 1997 ICC Trophy. Overall, in 9 matches, he took 19 wickets at an average of 10.68. His best 4/25 came in the Semi-Final against Scotland. With his spinning partner Enamul Haque Moni taking 12 wickets in the tournament. In the final against Kenya he had 26 of 15 deliverie.
Rafique was banned—with 13 professional players—for ten years from all forms of cricket by the Bangladesh Cricket Board following his enrolment in the Indian Cricket League (ICL) in August 2008, but renounced his ties with the ICL a year later and has since been accepted back into the fold. He is still playing first-class cricket for Dhaka Division and recently starred in the Big Boss T20 Premier League with a match-winning performance for Abahani Limited in the final.  However the players announced their departures from the Indian Cricket League in June 2009
A slow-left-arm orthodox bowler, Rafique was one of the few Bangladeshi players in the ICC bowler rankings' top fifty. He has become a permanent fixture in the national team, and is a household name in Bangladesh. He has achieved the double of 100 wickets and 1000 runs in both formats.
One of the most senior players in the Bangladesh team, Rafique was better known for his abilities in ODIs early in his career. He was nevertheless selected to play in Bangladesh's inaugural Test against India, and showed his promise with three wickets.
His career was almost derailed soon afterwards, when he was reported to the ICC for a suspect action. He was tardy in taking remedial action, and was out of the national team until 2002, when he was picked for the home series against South Africa. His return to cricket was classy and promising, with a six-wicket haul in the second Test against South Africa. He was the highest wicket-taker for Bangladesh in the home Test series against India, and the second highest during the away tour to Zimbabwe.
Rafique is also known as a handy, hard-hitting lower-order batsman. His 77 versus Kenya in May 1998 at Hyderabad was instrumental in Bangladesh's first ever ODI win against Kenya. With the ball, he took 3/56, and was adjudged the man of the match. He also scored a Test century against the West Indies in Bangladesh's drawn Test. Also he scored 65 against Australia in 2005-6, including six sixes.
He was instrumental in steering Bangladesh to a series whitewash against the Kenyans, and recorded his best match figures in Tests against Australia in a match they only narrowly lost. Rafique had a successful 2007 World Cup, taking eight wickets and helping Bangladesh to win games against India and South Africa.
Rafique announced his international retirement on 7 February 2008. Bangladesh's home series against South Africa was his last for the national team. He became the first Bangladeshi to ever take the milestone of 100 test wickets by having Robin Peterson caught at first slip by Junaid Siddique on 1 March during the second test. Out of 53 players who have scored 1,000 runs and taken 100 wickets in Test cricket, Rafique was the first to have represented Bangladesh.