Setiawan made his first appearance in the Thomas Cup in 2006. The Indonesian men's team eventually finished 3rd, losing to China in the semi-finals 0–3. At the 2006 Indonesia Open, ranked 14th in the world, Setiawan and Kido advanced to the final of the 2006 Indonesia Open after beating Jung Jae-sung and Lee Yong-dae of South Korea in the semi-finals. They were unable to defend their title after being defeated by the 2000 Olympic champions, Tony Gunawan and Candra Wijaya in the final. Bouncing back from the loss, they later won their first title of the year in the Hong Kong Open. At the 2006 World Championships, Setiawan and Kido lost in the quarter-finals to England's Robert Blair and Anthony Clark. This was their second loss to Blair and Clark, where earlier in the year they were also beaten in the second round of the All England Open. In October, Setiawan and Kido, then ranked 9th in the world, won the China Open by beating reigning World champions Cai Yun and Fu Haifeng in the final in straight games. Setiawan and Kido then claimed the 2006 World Cup, beating the Malaysian pairing of Lin Woon Fui and Fairuzizuan Tazari in the final. He competed in the 2006 Asian Games in Doha, Qatar, but lost in the semi-finals of both the men's doubles with Kido and in the men's team, settling for bronze medals in both events.
