At 2011 Skate Canada International, Takahashi earned a score of 84.66 in short program and 153.21 in free skating to win the bronze medal with a combined score of 237.87. At the 2011 NHK Trophy, he earned a new personal best score of 90.43 to take the lead in short program, with a 10.66 point lead over teammate Takahiko Kozuka. He won the gold medal with a combined total of 259.75 points and qualified for the Grand Prix Final. He finished second at the Final. At the Japanese Championships, Takahashi was first after short program with a score of 96.05 and placed third in free skating, scoring 158.38 points. With a total score of 254.60, he won his fifth national title, finishing ahead of Takahiko Kozuka and Yuzuru Hanyu, and was selected to compete at the 2012 World Championships, where he won the silver medal. The French crowd believed he had deserved the gold medal over Patrick Chan who had mistakes, including a fall on a double Axel, and booed the final result. Takahashi though stated that he was pleased with the result, which he had not expected after his off-season surgery. Takahashi finished the season at the 2012 World Team Trophy. He set new personal best scores in the short program, free skating, and overall, and finished first in the men's event. His short program score, 94.00, set a new record as the highest ever under the ISU Judging System. It was Takahashi's first win over Patrick Chan since the 2010 World Championships.