From 1998 to 1999 Prüfer-Storcks was Deputy Secretary of State of Karl Pröbsting in the State Ministry of Women, Youth, Family and Health of North Rhine-Westphalia. After his death in 1999, she was appointed his successor. Until the change of government in 2005, Prüfer-Storcks was State Secretary in the Ministry, which was renamed the State Ministry of Health, Social Affairs, Women and Family in 2002 as part of the reorganization of the ministries. From 2007 until her appointment to the Hamburg Senate, she was a member of the board of the health insurance of AOK Rheinland / Hamburg.
Following the 2011 state elections, Prüfer-Storcks has been Senator of the city state of Hamburg. From 23 March to 30 April 2011, she was President of the Department of Social Affairs, Family, Health and Consumer Protection for the sector of Health and Consumer Protection. After hiving off individual departments and the new formation of the Authority for Health and Consumer Protection,[2] she took over on 1 May 2011 as President of this authority. As one of the state’s representatives at the Bundesrat since 2011, she is a member of the Committee on Health.
In the negotiations to form a Grand Coalition of Chancellor Angela Merkel's Christian Democrats (CDU together with the Bavarian CSU) and the SPD following the 2013 federal elections, Prüfer-Storcks was part of the SPD delegation in the working group on health policy, led by Jens Spahn and Karl Lauterbach. Appointed by Federal Minister of Health Hermann Gröhe, she served as member of an expert commission on the reform of Germany’s hospital care from 2015 until 2017.[3]