He began his professional football career, playing for his hometown club, Tractor Sazi, following footsteps of his brother, Hossein Khatibi. He was able to impress, and after scoring many goals for his club, he was transferred to Pas Tehran. He continued to play well, giving himself a chance to join Hamburger SV in the Bundesliga along with fellow Iranian internationals Mehdi Mahdavikia and Vahid Hashemian.
While playing in Hamburg, he only had a couple of appearances, and was not able to make good use of his chances. He soon returned to Iran, back to his old club, Pas. He then briefly played for Esteghlal in the Asian Champions League before signing for Sepahan. Sepahan was able to win the IPL championship in 2003 and Khatibi started showing his good form again. In the 2005–06 season, he was able to score ten goals, completing his impressive record in Sepahan with 32 goals in three seasons. His tally would have been higher if not for his poor chances to goals ratio. In June 2006, he signed a two year contract with UAE club, Sharjah FC, after rejecting an offer from Spanish second division side CD Tenerife. In 2007, Khatibi signed a new contract with Emirates for $700,000 to join his Iranian team-mate Reza Enayati. The contract has a clause which states that if a European club offers Khatibi a contract, then the existing contract with Emirates Club will be canceled. He then joined Gostaresh Foolad as player-manager. He announced his retirement on 5 August 2013.
Khatibi has played for Iranian national teams of various age levels. He was a constant member of the Iran Olympic team team during his time in Teraktor Sazi and Pas, but despite the talent on the team, they were never successful. He gained his first international cap on 15 February 1999 versus Kuwait. His appearances for the national team have been inconsistent, but due to his good form in the 2005–06 season he was called up to the main squad which headed to Germany for World Cup 2006. He has 24 caps and 5 goals for the national team.
After joined Machine Sazi in summer 2011, he becomes player-manager of Machine Sazi Tabriz on 1 July 2011 to lead the team in Azadegan league. After spending one season at Machine Sazi and led them to the third rank and lost the promotion play-off on goal difference, he becomes head coach of another Tabrizi based team, Gostaresh Foolad and led the club to promotion to the Iran Pro League. He renewed his contract for another three seasons on 13 May 2013 but resigned on 26 December 2013 after a run of unsuccessful results.
On 31 May 2014, Khatibi was appointed as new manager of Tractor Sazi, replaced Toni Oliveira. He signed a three-year contract with the club.