The school announced Monday he will return for his junior year.
The point guard was Notre Dame's second-leading scorer last season, averaging 18.7 points and a team-high 6.9 assists. He became the first player in school history to hand out more than 200 assists in back-to-back seasons.
"Now that he has gone through the process, I believe that he has made a great decision to return to Notre Dame," Fighting Irish Coach Mike Brey said. "I feel very strongly that when Chris' time comes, he is going to have a great 8-10 year career in the NBA."
The 6-1 Thomas already ranks fifth on the school's all-time assists list with 488, averaging 7.3 per game.