Phelps last won a 200 fly race at the 2012 Olympic trials and declared he would not return to the event when he came out of retirement last year.
"I was happy to give a good effort," Phelps said. "In my whole career, I never trained more than a 100 fly. I'm doing things in workouts for the fly that I haven't done before. It's good to have my confidence back."
Phelps swam his first 200 fly since earning a silver medal in London last month in Charlotte, finishing seventh in 2 minutes, 0.77 of a second.
Still the world-record holder in the event, Phelps seems determined to recapture the glory of the event that vaulted him into prominence at the 2000 Olympics.
He won Saturday in 1:57.62, six seconds slower than his record time in Rome in 2009 but three seconds faster than last month. It was the time he targeted to continue working out for the event.
"I swam in aggressively, and it's kind of weird to say but hard work does pay off," Phelps said. "From here I go to Colorado Springs for three weeks of training to get into even better shape and get ready for nationals."
Phelps' North Baltimore teammate Chase Kalisz, who won in Charlotte, finished second in 1:58.06.
"I finally won a race and I wanted to go 1:57 so I am very pleased with the race," Phelps said. "I was trying to come home and saw Chase's splashes and wanted to do everything I could not to let him beat me."
Phelps, who turns 30 at the end of the month, already owns 18 Olympic gold medals and 22 medals overall as the most decorated Olympic swimmer. He has set a record 39 world records, 29 in individual races, and still owns seven.
Olympian Connor Jaeger overtook Phelps in the final 50 meters to win the 200 free in a personal-best 1:48.66. "That was probably the fastest last 50 I've ever done," he said. "If you're looking for extra motivation there's nothing like diving in next to the greatest of all time."