In 2004 she competed in the Athens Olympics, placing 4th in the 100 m butterfly with the time of 58.22 s. She also collected the gold medal in the 4x100 m medley relay, having swum the butterfly leg in the heats of the event.
At the 2005 World Aquatics Championships in Montreal, she won the silver medal in the 200 m butterfly with the time of 2.05.65 s, only 0.04 seconds behind Otylia Jędrzejczak of Poland, who consequently recorded a new world record in the event. However, the race was overshadowed by the video replay showing that Jędrzejczak touched the finishing wall with only one hand, which is illegal under the butterfly rules. Doing so allows the swimmer to stretch out further with their single hand. Video replays cannot be used in appeals against race results. Schipper also won the gold in the 100 m butterfly (57.23 s) and in the 4×100 m medley relay, with teammates Sophie Edington, Leisel Jones and Libby Lenton. In doing so, she erased the Australian records in both the 100 m and 200 m butterfly set by Petria Thomas and Susie O'Neill, respectively.
In 2006 Schipper wiped 0.08 s off her 100 m butterfly (57.15 s) Commonwealth record to become the second fastest woman ever in the history of the event, surpassing Martina Moravcová.
She won the gold medal in both the 100 m and 200 m butterfly as well as the silver medal in 50 m butterfly at the 2006 Commonwealth Games held in Melbourne. She combined with Sophie Edington, Leisel Jones and Libby Lenton to set a new world record in the 4×100 m medley relay, collecting her third gold medal of the meet.
Schipper qualified for the 100 m and 200 m butterfly events in Beijing, where she is among the favourites for the medals. She is a member of the 4×100 m medley relay squad. Schipper won two bronze medals in her individual events at the Beijing Olympics, the 100 m and 200 m butterfly. Schipper also won gold in the 4×100 m medley relay team with teammates Leisel Jones, Libby Trickett and Emily Seebohm.
Following the Olympics, Schipper split with her coach Ken Wood. This came after Wood had sold Schipper's training program to Chinese swimmer Liu Zige, who broke Schipper's world record to take the 200 m title. She then joined the Commercial Swimming Club in Brisbane, under Stephan Widmar, who previously coached her Australian relay teammates Leisel Jones and Trickett.
Schipper maintained her consistency at the world championship level. On day two, she took silver in the 100 m butterfly, clocking the second fastest time in history. On day five she retained her 200 m butterfly title in world record time, defeating Liu Zige by 0.49s.
In 2012, Schipper again qualified for the 100 m and 200 m butterfly events. She was eliminated in the heats of the 100 m. She qualified for the semifinal of the 200 m, but not for the final. Her 200 m semifinal time of 2:08.21 was nearly 5 seconds slower than her best time in that event.