Paintsil was a member of the Ghana Under 21 team who were runner-up in the FIFA World Youth Championship in Argentina in 2001 and played for the senior team in the African Cup of Nations in Mali in 2002 and Egypt in 2006. He was also a member of the Ghana 2004 Olympics football team who exited in the first round in Greece, having finished in third place in Group B. Paintsil played in all the matches of Ghana's national team in the 2006 World Cup finals, where Ghana were beaten by Brazil in the second round.