After completing high school (Abitur), he studied chemistry, biology and physics at the University of Heidelberg. Following completion of his doctorate and habilitation he became a university professor in Heidelberg and, at the same time, became the head of a department at the German Cancer Research Center. In 1982, Franke became the president of the European Cell Biology Organization (ECBO), a post he held until 1990.
He is considered a leading expert in performance-enhancing drugs and one of the most ardent critics of drug abuse in sports. Together with his wife, Brigitte Berendonk, once an Olympic discus thrower and shot putter, he has fought against drug abuse in sports. He assisted his wife in researching the 1991 book Doping: From Research to Deceit, uncovering the systematic use of doping by East German athletes.
Franke defended cyclist Danilo Hondo after the banned substance Carphedon was found in his blood during the 2005 Vuelta a Murcia. Franke argued that the amount found in his blood was "laughably small" and that "you can only get this medication through certain channels in Russia or China, where it is used by the military and the space flight programs."
During an interview on 3 August 2006 with German regional television channel Rheinmaintv, Franke claimed that cyclist Jan Ullrich purchased about EUR35,000 worth of doping products a year based on documents uncovered in the Operación Puerto doping case. A German court imposed a gag order on Franke after it found there was not enough evidence to link Ullrich to doping. However that case is returning to court since DNA analysis linked Ullrich to nine bags of blood seized in the Puerto case.