Stewart got off to a scary start for the 2001 season: during the Daytona 500, he was involved in an 18-car crash on lap 173. Stewart took the worst of it, as his car turned backward after being hit by Ward Burton, pushed over by Robby Gordon, then flipped twice in midair, hooked Bobby Labonte's hood, and came to a stop in the infield. Stewart was transported to Halifax Medical Center after complaints of discomfort in his shoulder. Stewart's crash was greatly overshadowed by Dale Earnhardt's fatal crash on the last lap. Stewart recovered to win three more races at Richmond, Infineon, and Bristol and, as he had done before, he ran near the front most of the season. Statistically, he had a worse season than 2000, but he finished 2nd to Gordon in the final points standings.

The 2001 season was not without controversy. Jeff Gordon pulled a "bump and run" on Stewart to gain a better finishing position at Bristol and Stewart retaliated in a post-race incident by spinning Gordon out on pit road. Stewart was fined and placed on NASCAR probation. He got into much bigger trouble in the Pepsi 400 at Daytona, where he confronted a Winston Cup official after ignoring a black flag, which he had received for an illegal pass on Dave Blaney. He confronted that same official during the Talladega race after he refused to wear a mandated head-and-neck restraint. Stewart was not allowed to practice until he wore one, and only managed to do so after his crew chief Greg Zipadelli intervened. Stewart's fines and periods of probation resulting from these incidents have earned him a reputation of having a hot temper, and he became known as NASCAR's "bad boy".