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.