Phelps, who has held the world record in the event since 2001, covered the distance Thursday in 1:53.65. That was the best time in the world this year, but was well short of his world mark of 1:51.51.
"It's decent," Phelps said. "But I think it will take better than that to win the (Olympic) gold medal."
Tyler Clary finished second in the time of 1:55.12 to make his first Olympic team.
Phelps has officially qualified in three events and could swim in as many as 10 races at next month's Olympics in London. He holds the record for most Olympic gold medals in one Games (eight) and for a career (14).
In the other finals held Thursday, Allison Schmidt set an American record of 1:54.40 to capture the 200-meter freestyle and Caitlin Leverenz won the 200-meter individual medley in 2:10.22.
Schmidt added the 200-meter freestyle victory to her 400-meter freestyle triumph earlier in the trials.
Missy Franklin earned her way onto the Olympic team in her second event by finishing second to Schmidt and Ariana Kukors was runner-up to Leverenz in the individual medley.
Trader Joe's: Car crashes into Long Island store, injuring 11
Wisconsin business offering 'therapeutic cuddling' forced to close