Additionally, Nekounam helped Iran win the 2002 Asian Games and the 2004 West Asian Football Federation Championship, and also represented the country in the 2004, 2007 and 2011 AFC Asian Cups. He was "Team Melli"'s leading goalscorer in its successful 2014 World Cup qualifying campaign and, on 1 June 2014, he was selected by Carlos Queiroz for the finals in Brazil, where he captained the nation in an eventual group-stage exit.