- 1987 – Doctor of Medicine degree from the University of Amsterdam
- 1987-1988 – Officer of the Royal Netherlands Air Force Medical Corps
- 1989-1999 – Worked for the Research and Development department of the Netherlands Aerospace Medical Centre in Soesterberg
- 1999 – Joined the ESA Astronaut Corps, ESA Astronaut on two missions between 2004 and 2012
During his time at the Netherlands Aerospace Medical Centre Kuipers was involved in the physiological ESA experiments for space missions, including the Spacelab-D2 mission in 1993, the EuroMir-95 mission and the LMS Spacelab mission in 1996.
In July 1999, Kuipers joined the ESA’s Astronaut Corps and was assigned to ESTEC, continuing his work on microgravity experiments.
During Soyuz missions Soyuz 6S and 7S to the International Space Station he supported ESA's ground team from the Russian Control Centre as Crew Interface Coordinator and was also backup for ESA astronaut Pedro Duque’s mission in October 2003.
In 2002, Kuipers was assigned as a Flight Engineer for a Soyuz flight to the International Space Station on the DELTA mission, which took place in April 2004 and where he performed 21 experiments in human physiology, biology, technology and education.
From 2007, he trained as backup to ESA astronaut Frank De Winne for Europe’s second long-duration spaceflight to the International Space Station : from May 2009, Kuipers was assigned to Eurocom duties at the Columbus Control Centre and EAC in support of De Winne’s six-month mission.
He was later assigned to Expedition 30/31, a long-duration mission to the International Space Station called PromISSe, launched in December 2011 from Baikonur Cosmodrome in Kazakhstan. During his mission, he took part in around 50 experiments covering a wide range of disciplines and returned to Earth in July 2012.