At the age of 14, Seebohm won the 100 m backstroke at the 2007 Australian Championships, the selection meet for the 2007 World Aquatics Championships. At the World Championships in Melbourne, Seebohm won a gold medal in the 4 × 100 m medley relay. She also placed fourth in the final of the 100 m backstroke and 14th in the 50 m backstroke.
Seebohm also won gold in both the 100 m backstroke and 4 × 100 m medley relay at the 2007 Junior Pan Pacific Swimming Championships.
On 6 March 2008 at the Brisbane Catholic Schoolgirls Championships, Seebohm broke the 50 m backstroke Commonwealth and Australian records with a time 28.10 seconds, missing Li Yang's then world record of 28.09 by one hundredth of a second.
On 22 March 2008, Seebohm broke the world record in the 50 m backstroke in the semi-finals of the 2008 Australian Championships, with a time of 27.95s, taking five hundredths of a second off Hayley McGregory's world record of 28.00 set only 15 days earlier on 7 March 2008. A day later, this record was beaten again, this time by Australian Sophie Edington in a time of 27.67 seconds in the final of the same event. Seebohm decided not to swim in the final of this event as it is not an Olympic event and instead decided to focus on the semi-final of the 100 m backstroke. Her decision paid off when she became the first Australian woman to break the one-minute barrier in the event, her 59.78 making her the fifth-fastest of all-time. She then lowered the record to 59.58 s in the final, winning the Australian championship and gaining selection for the Olympic Games in Beijing.
At the 2008 Summer Olympics, Seebohm placed ninth overall in the 100 m backstroke, barely missing a spot in the final. Seebohm then swam in both the preliminaries and final of the 4 × 100 m medley relay, in which Australia won the gold medal.
At the 2009 World Aquatics Championships in Rome, Seebohm won the bronze medal in the 100 m backstroke with a time of 58.88. She also won silver in the 4 × 100 m medley relay, and placed 7th in the 50 m backstroke and 15th in the 200 m IM.
When Seebohm was three she moved with her family from Adelaide to Brisbane, Queensland so her mother could coach swimming. Seebohm attended St Joseph's Catholic Primary School until Grade 6, and then moved on to St John Fisher College, a Catholic school for girls. Both schools are in Bracken Ridge. She attended St John Fisher College up until the end of 2008, where she completed grade 10, and previously attended St Margaret's Anglican Girls School. Her father John Seebohm was also an accomplished footballer in the SANFL, who played over 300 games for the Glenelg Tigers.
On 26 January 2009, Seebohm was awarded the Medal of the Order of Australia.
In 2015, Seebohm began a relationship with fellow swimmer, Mitch Larkin. The couple owned a house together in Hendra, Brisbane. In July 2018, Seebohm announced their separation. In January 2019 Emily announced that she has entered into a new relationship with the well known Australian Actor, Brett Hinch. They have recently purchased a house together in Sydney.