Bagheri was first called up to the Iranian national team during the 1994 FIFA World Cup qualifiers, making his debut versus Pakistan on 6 June 1993. He displayed great football and soon became a starter for Iran in the midfield. He played in 1996 AFC Asian Cup for Team Melli and finished third.

Bagheri was born in Tabriz, Iran. He was discovered by manager Vasile Godja and began his football playing for his hometown club Tractor where he impressed enough to land himself a contract with Keshavarz On 1 August 1996 Bagheri was signed on free transfer by the capital’s club, Persepolis. There, Bagheri enjoyed much success winning numerous titles and becoming a fan favorite. Numerous impressive displays ended up in Bagheri attracting attention from many European clubs and on 1 August 1997, a year after he signed a contract with Persepolis, Bagheri signed with German Bundesliga side Arminia Bielefeld along with his fellow Iranian international Ali Daei.

He sparked Iran’s comeback against Australia in the second leg of their 1998 FIFA World Cup qualifier in 1997. He scored the first of two goals that took Iran from two goals down to tie the game 2–2 and eventually become the last team to qualify for the tournament. Overall, he scored 19 goals during the 1998 FIFA World Cup qualification campaign, making him the top goalscorer from all six continental confederations. He played in 1998 Asian Games and won the competition. Bagheri also had one of the strongest right-footed shots and scored many fantastic goals against opponents, such as his game-tying goal against South Korea in the quarter finals of the 2000 Asian Cup in Lebanon.

On 2 June 1997, he scored seven times against the Maldives, and equalled the record for the most goals scored in a World Cup match, which was held by the Australian Gary Cole since 1981. Their joint record was broken on 11 April 2001 when another Australian, Archie Thompson scored 13 goals against American Samoa. He was named the world’s second top goal scorer in official international matches by International Federation of Football History and Statistics (IFFHS), having scored 20 goals for Iran in 1997.

He retired from the national team with 80 caps and 47 goals for Team Melli after Iran’s unsuccessful FIFA World Cup 2002 qualification campaign which ended with an aggregate defeat to Republic of Ireland in November 2001. He was called up to the national team again soon after World Cup 2006, but said he would not participate as he is retired from international football and has no plans on returning to it.

In 2002, he decided to return to Persepolis once again. In September 2006, many thought he had been released from the team after arguments with management and staff over the club’s financial commitments and unpaid wages. Bagheri was instead disciplined but remained on the team. Bagheri has since established himself as one of the greatest icons of Persepolis and many compare his popularity with Ali Parvin. In the 2007–08 season, he captained the team to glory in the IPL after a six-year drought. During the 2008–09 season he was injured and missed many matches. He also missed matches because of the differences he had with the coach Nelo Vingada at the end of the season. He was the top scorer of the team for 2009–10 season and the most influential player on the team. In the second Sorkhabi derby of the season, Bagheri scored in the 87th minute with a trademark long-range shot to gain victory for Persepolis after six consecutive draws in the derby.

On 9 October 2008, Team Melli coach Ali Daei stated that because of Andranik Teymourian’s injury Bagheri will be called up for the national team once again. On 9 November 2008 in a friendly match against Qatar, he appeared for Team Melli once again after almost seven years. Bagheri captained Iran in the 2010 FIFA World Cup qualification match against UAE on 19 November 2008, scoring for Iran. He has been given his favorite number 6 jersey back. He played few important matches for Team Melli in 2010 FIFA World Cup qualification against UAE and South Korea. He was invited again by Afshin Ghotbi but he stated in Navad that he only returned to Team Melli because of Ali Daei and will not participate in any more matches for Team Melli.

On 1 December 2010, Bagheri announced that he would retire and leave Persepolis.

On 2 October 2010, Bagheri announced he would play his last match with Team Melli on 7 October 2010 against Brazil in the Sheikh Zayed Stadium in Abu Dhabi, United Arab Emirates.

On 8 April 2015, Karim was named assistant manager of Persepolis again.