Thoman was born in Cincinnati, Ohio. He swam for Cincinnati Aquatic Club under head coach Benson Spurling from age 8 through high school. He attended Mariemont High School in the suburbs of Cincinnati and was coached by Kevin Maness. At the 2009 Duel in the Pool, a short course meet, Thoman combined with Mark Gangloff, Michael Phelps, and Nathan Adrian in 4×100-meter medley relay to break the world record previously held by Canada. While leading off the relay, Thoman also broke the world record in the 100-meter backstroke with a time of 48.94. At the 2010 National Championships, Thoman qualified to swim at the 2010 Pan Pacific Swimming Championships in the 50, 100 and 200-meter backstroke. In the 100-meter backstroke final at the 2010 National Championships, Thoman was out first at the first 50 with a time of 25.80. However, he faded to third place with a time of 53.78, finishing behind David Plummer and Aaron Peirsol. In the 200-meter backstroke final, Thoman finished in 5th place with a time of 1:57.7. At the 2010 Pan Pacific Swimming Championships, Thoman won bronze in the 50-meter backstroke. At the 2010 FINA Short Course World Championships in Dubai, Thoman won a gold medal in the 4×100-meter medley relay with Mihail Alexandrov, Ryan Lochte, and Garrett Weber-Gale. Thoman also competed in the 50 and 100-meter backstroke in Dubai but finished out of medal contention in both events. At the 2011 World Aquatics Championships in Shanghai, China, Thoman placed fourth in the final of the 100-meter backstroke with a time of 53.01. In the 4×100-meter medley relay with Mark Gangloff, Michael Phelps, and Nathan Adrian, Thoman won gold with a time of 3:32.06. Swimming the backstroke leg, Thoman had a time of 53.61.
At the 2012 U.S. Olympic Trials in Omaha, Nebraska, the U.S. qualifying meet for the Olympics, Thoman made the U.S. Olympic team for the first time by finishing second in the 100-meter backstroke in a time of 52.86. Thoman also placed third in the 200-meter backstroke with a time of 1:57.06, missing a spot in that event. At the 2012 Summer Olympics in London, Thoman won his inaugural Olympic medal, a silver, in the 100-meter backstroke. In the final, Thoman placed second behind fellow American Matt Grevers with a time of 52.92. He also earned a gold medal swimming the backstroke leg for the winning U.S. team in the preliminaries of the 4×100-meter medley relay.