Takahashi presented his new free skating for the season at the 2012 Japan Open. It was the first time since his injury that he performed two quad jumps in his free skating. He placed first in the men's event and Japan took the team gold medal. He switched to new skating boots just after returning from training in the U.S. in October. This affected his practice schedule leading up to his Grand Prix events. Takahashi said: "The shoes happened to be uncomfortable beyond my expectations, which attributed to difficulty in blade adjustments. As a result, I was not able to practice as I had scheduled." At the 2012 Cup of China, his first Grand Prix event of the season, he won the silver medal behind Tatsuki Machida. Takahashi won the silver medal at his next Grand Prix event, the 2012 NHK Trophy, and qualified for his seventh Grand Prix Final. The 2012 Grand Prix Final took place in Sochi, Russia at the planned 2014 Winter Olympics rink. Takahashi placed first in short program and third in free skating and won his first GPF gold medal. He is also the first Japanese man ever to win a gold medal at the Grand Prix Final.