On January 4 at Wrestle Kingdom III in Tokyo Dome, Tanahashi defeated his mentor Keiji Mutoh to become the 50th IWGP Heavyweight Champion, beginning his third reign. Following his victory, when asked who he would like his next challenger to be, Tanahashi called out generation rival Shinsuke Nakamura, who accepted. At New Japan's ISM tour on February 15, Tanahashi defeated Nakamura with the High Fly Flow in his first title defense. Tanahashi defeated Kurt Angle on April 5 at New Japan's "Resolution 09" with two High Fly Flows. His next opponent was Hirooki Goto, whom he defeated on May 3 at Wrestling Dontaku 2009 with a High Fly Flow. Just days later, Tanahashi was defeated by Manabu Nakanishi on May 6 at "Dissidence 2009". He regained the Title from Nakanishi on June 20 at Dominion 6.20 for his fourth reign. He successfully defended the title against Pro Wrestling Noah's Takashi Sugiura on July 20, the first ever NJPW vs. Noah match for the IWGP Heavyweight title. During a post-match interview, Tanahashi was interrupted by Tajiri, who then sprayed Tanahashi with Green Mist. Tanahashi would vacate the IWGP Heavyweight title on August 17, due to an eye fracture injury he suffered in a match with Shinsuke Nakamura, in the semi-finals of the 2009 G1 Climax Tournament. On November 8 at Destruction '09 Tanahashi returned to challenge for the belt he was forced to vacate, but came up short against the reigning champion Nakamura. On December 5 Tanahashi would avenge the loss he suffered during the G1 Climax Tournament and end his feud with Tajiri by pinning him in a singles match with the High Fly Flow. Afterwards, Tanahashi made a challenge to Pro Wrestling Noah and on January 4, 2010, at Wrestle Kingdom IV in Tokyo Dome he defeated Noah's Go Shiozaki in a match that was billed as "Ace vs. Ace". Since then, Tanahashi would begin a feud with Toru Yano, starting with Yano upsetting Tanahashi in a tag team match on January 30, where he teamed with Manabu Nakanishi and Yano with Shinsuke Nakamura. On February 14, Tanahashi avenged his loss in a singles match with Yano, but was jumped after the match by Masato Tanaka, after which Yano proceeded to cut off some of his hair. After Yano defeated Tanahashi in a singles match at Wrestling Dontaku 2010, New Japan booked the two men in a Hair vs. Hair match for June 19. On June 19 at Dominion 6.19, Tanahashi defeated Yano and was afterwards assisted by former rival Tajiri and Kushida in taking care of Yano's ally Takashi Iizuka and shave his opponent's hair. In August, Tanahashi entered the 2010 G1 Climax tournament and made it all the way to the finals, after four wins and a draw in the round robin stage of the tournament. However, in the finals Tanahashi was defeated by freelancer Satoshi Kojima. In October and November 2010, Tanahashi teamed with Tajiri in New Japan's 2010 G1 Tag League. After a strong start in the tournament, Tanahashi and Tajiri were defeated by the IWGP Tag Team Champions Bad Intentions (Giant Bernard and Karl Anderson) on November 6, the last day of group stages, and slipped to third place in their block, narrowly missing the semifinals of the tournament.
