During her rise to stardom surrounding the 2012 Olympics, Franklin continued to refuse prize money and endorsements so that she could maintain her amateur status to compete in college. In 2012, she accepted an athletic scholarship to attend the University of California, Berkeley, where she began swimming for coach Teri McKeever's California Golden Bears women's swimming team during the 2013–14 academic year. At Cal, Franklin is a four-time individual NCAA champion: winning the 200-yard freestyle in 2014 and 2015, and the 200-yard backstroke and individual medley in 2015. She won the Honda Sports Award as the nation's top female swimmer in 2015, as well as the Honda Cup awarded to the nation's top female athlete. She transferred from the University of California, Berkeley to the University of Georgia. After the 2015 NCAA Swimming and Diving Championships, in which Franklin won three individual NCAA titles, Franklin turned professional. She graduated with a degree in religion from the University of Georgia in December 2019.
At the 2012 United States Olympic Trials, Franklin qualified to swim in four individual events at the 2012 Summer Olympics. In her first event, the 100-meter backstroke, Franklin won the final with a time of 58.85, breaking Natalie Coughlin's American record of 58.94 seconds. In her second event, the 200-meter freestyle, Franklin placed second behind Allison Schmitt by over two seconds with a time of 1:56.79. In her third individual event, Franklin finished second in the 100-meter freestyle behind Jessica Hardy with a time of 54.15. Her second-place finish came less than half an hour after swimming in the 200-meter backstroke semi-finals, where she finished first overall with a time of 2:07.91. In the 200-meter backstroke final, her fourth individual event, Franklin finished first with a time of 2:06.12.