In August 2005, he made his international debut when he was in charge of a Rugby World Cup qualifying match between Uganda and Zimbabwe in Kampala. In June 2006 he refereed the Pacific Nations Cup match between the Junior all Blacks and Samoa and the mid-year international between Fiji and Italy. In November he was the referee for the Autumn International between Ireland and Australia, which was the last game to be played at the old Lansdowne Road ground. In March 2007 he took charge of his first Six Nations match, the Calcutta Cup match between Scotland and England. A month later, despite having handled only seven internationals, Jonker was named as one of three 'debutants' (the others were Wayne Barnes of England and Nigel Owens of Wales) in the 12-man panel of referees for the pool stages of the 2007 Rugby World Cup; he refereed three games, including Scotland v New Zealand, and was one of the touch judges for the semi-final between England and France.