He was named as part of the New Zealand squad for the 2009 FIFA Confederations Cup in June 2009. He made two starting appearances at right-back in defeats to Spain and South Africa, as well as a substitute appearance in the 0–0 draw with Iraq. Mulligan was named in New Zealand's final 23-man squad to compete at the 2010 FIFA World Cup in South Africa; he had been selected by head coach Ricki Herbert despite Herbert having released him at Wellington Phoenix. However he did not feature in any of the games in the tournament itself.