Cheika was appointed as head coach of the New South Wales Waratahs in 2012 for the 2013 Super Rugby season. In his first season, he guided the team to mid-table of 9th, with an even split of 8 wins and 8 losses. Some of their victories were notable, including the 25–20 win over the eventual (and defending) champions, the Chiefs, in round 10. The Waratahs turned over the Brumbies 28–22, before narrowly losing to the Crusaders 23–22 in Christchurch. Cheika also led the team against the British and Irish Lions, losing the match 47–17. He was responsible for signing Israel Folau from AFL side Greater Western Sydney Giants, who made a massive impact to the Wallabies in his debut season.