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2020–21 season: Seventh world medal

In 2021, due to travel restrictions related to the coronavirus pandemic, Hanyu started to train alone in Sendai with some remote consultation from his coaches. Despite the difficulties of training alone, Hanyu found that it had been a good opportunity to learn how to control and analyze himself, which led him not return to Canada until he turned professional and made Ice Rink Sendai his training base again. Hanyu also opted to receive remote choreography for his programs ever since and has contributed significantly to the choreography of his programs in the 2020–21 season. On August 28, he announced that he would skip the Grand Prix series, citing the risk of COVID-19 for himself, the competition staff, and for his fans who would gather to support him. Despite feeling "conflicted" over whether he should have competed or not as COVID-19 continued and practicing without his coaching team, Hanyu decided to compete in Japanese championships, which doubled as the final qualifier for the upcoming World Championships in Stockholm. He placed first in the short program (103.53 points) and the free skate (215.83 points) with all positive grades of execution on jumping passes and won his fifth national figure skating title with a total score of 319.36 points.

The 2021 World Championships were to be the first direct competition between Hanyu and Nathan Chen since the 2019–20 Grand Prix Final. Hanyu placed first in the short program with a solid performance, 6.02 points ahead of compatriot Yuma Kagiyama. In the free skate, Hanyu opened his program with two quadruple jumps and a triple Axel but received negative grades of execution for all three of them. Scoring 182.20 points, he placed fourth in the free skate and third overall, behind Chen and Kagiyama. It was the first competition Hanyu had placed below second since 2014, however, he became the first male single skater besides German Jan Hoffmann to win seven World medals in the post-war era since 1946. On the following day, Hanyu confirmed the report of his asthma attack by overseas media. He stated that he felt a little painful after finishing the free skate, and explained: "There were few small troubles that kept stacking up... However, if asked whether that was what led to the huge mistake (in the free skate), I don't think it was as big of a miss as it was in terms of the miss in the score." Hanyu's placement combined with Kagiyama's qualified three berths for Japanese men at the 2022 Winter Olympics. Hanyu competed as part of Team Japan for the 2021 World Team Trophy. He placed second in both the short program and the free skate, only behind Nathan Chen. He achieved a personal season's best score in both the short program and the free skate with 107.12 and 193.76 points respectively and earned a total of 22 points to help his team take home the bronze medal.