The 18-year-old swam the opening, backstroke leg in the hilltop pool in Barcelona and the US triumph followed her titles this week in 100 and 200 backstroke, 200 freestyle and the 4x100 and 4x200 freestyle relays.
She was fourth in Friday's 100 freestyle.
"It hurt really, really bad but now we're all done and we're all super excited," a still-dripping Franklin, who is due to sign on at University of California, Berkeley later this year, told reporters.
"I think I'm going to take my time off until I get to Berkeley so I think that gives me about two and a half weeks. We're all pretty excited about it."
Franklin's sixth gold is one more than the previous record of five she jointly held with compatriot Tracy Caulkins and Australia's Libby Trickett.
The only other woman to win six golds at a major swimming meet was East German Kristin Otto at the 1988 Olympics in Seoul.
After her three world titles at the 2011 championships in Shanghai, Franklin is also tied for the most golds overall with Trickett on nine.
Photograph: Alexander Hassenstein/Getty Images