Between 2004 and 2007, Courtney refereed three matches in the Six Nations Championship. He made his Six Nations debut on 14 February 2004 when he took charge of a match between Wales and Scotland. On 19 March 2005 he refereed a match between Italy and France. In addition to refereeing, Courtney also served as a television match official and touch judge in the Six Nations. During the 2007 Six Nations Championship Courtney officiated at three of Scotland's matches. On 3 February 2007 he served as the TMO during the match between England and Scotland. He confirmed a try for England's Jonny Wilkinson despite video footage clearly showing that Wilkinson's foot had been in touch. At a post-match press conference, Scotland's coach, Frank Hadden, heavily criticised Courtney for his decision.