Having studied biology, Ekkehard Winter obtained a PhD in Molecular Biology from the Institute for Genetics, Cologne University. He began his professional career in 1988 as project manager at the Academy of Sciences and Technology, Berlin. In 1990, he moved to Essen to join the Stifterverband, an industry association for the advancement of higher education and research. Following a stay abroad at the Engineering and Physical Sciences Research Council (EPSRC) in Swindon, England, Ekkehart Winter was appointed head of the Stifterverband’s "Programme and Promotion" unit in 2000 and member of the executive board. In this position, he co-founded "Science in Dialogue" (Wissenschaft im Dialog, WiD), a science communication initiative of all German research organisations.
On 1 January 2003, Ekkehard Winter was named deputy general secretary of Stifterverband. On 1 February 2005, he joined Deutsche Telekom’s charitable foundation as executive director. The foundation which was established at the end of 2003 focuses its activities on improving education and teacher training in science, technology, engineering and mathematics (STEM). With a foundation capital of € 150 million, it is one of the biggest corporate foundations in Germany. Ekkehart Winter chairs several working groups in the Association of German Foundations and the National STEM Forum.