The Indiana meeting is doubling as trials for the world championships in Barcelona staring on July 28.
Franklin, who came from behind at the turn to beat Elizabeth Pelton in 58.67 seconds, had already qualified in the 100 and 200 freestyle, the 200 backstroke and earned a place in both the 4x100 and 4x200 freestyle relay squads.
"I think the whole field was right there at the 50," Franklin said after she pipped her future collegiate team mate Pelton by 0.6 seconds.
"I knew I had to bring it back that last half, so it was tough. It hurt a lot. It's the hardest, but that's my favourite part that last 15 metres."
Despite being the quickest in the world this year, the 18-year-old said she was looking for more improvement before the world championships.
"The main goal is to be faster in four weeks than we were right now," Franklin said.
"I think that's the goal for everyone. It will definitely be about the little technicalities the next four weeks."
"(Coach) Todd (Schmitz) and I will sit down and review what we need to do for each event, but I think for the most part, each event has different things I need to work on, which is fun.
"There's always room for improvement."
Fellow Olympic champion Katie Ledecky claimed the women's 400 freestyle with Chloe Sutton second while Connor Jaeger won the men's title with Matt McLean second.
Breeja Larson and Kevin Cordes backed up their wins in the women's and men's 200 breaststroke on Wednesday with victories in the 100.
David Plummer, who won the 50 backstroke on Thursday, qualified for the 100 by beating London Olympic champion Matt Grevers.
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- Elizabeth Pelton