Earlier in the day, Phelps also qualified in the 200-meter freestyle. The finals for both races will be held Saturday.
Phelps, the most decorated athlete in Olympic history, has returned from retirement with a lighter approach to swimming. Since making his first appearance at a Grand Prix event in Arizona last month, he has laughed and told jokes poolside.
Phelps has remained vague about his plans regarding the 2016 Rio de Janeiro Olympics. Maybe he gave a hint during a practice session in Charlotte this week. His orange swim cap read: "Rio 2016."