Franklin, who won four golds at the London Games last year, was the star attraction on the opening night of the event, which serves as the US trials for the July 19-August 4 World Championships.
The 18-year-old set a personal best, and championship record, time of 53.43 to win her race.
"Coming home, (my coach) Todd (Schmitz) told me to look at the field coming off the 50 wall and just put my head down and swim it my own way," Franklin said. "That's what I did."
Shannon Vreeland finished second in 53.83, followed by Simone Manuel and Megan Romano, who all booked their ticket to Spain.
On the men's side, Nathan Adrian, who won the 100 freestyle gold in London, won his race in 48.10, a time that did live up to his expectations.
"I would have loved to be under 48, but it wasn't there tonight," he said.
Other national champions crowned on the night included Cammile Adams and Tom Luchsinger in the 200m butterfly, Katie Ledecky in the women's 800m freestyle and Connor Jaeger in the men's 1500m.
- Sports & Recreation
- Megan Romano