Franz Hillenkamp was born in Essen, Germany. Having chosen the science and math track in the Gymnasium Hillenkamp went on to major in electrical engineering at Technische Universitat Munchen (TUM). He interrupted his diploma thesis on vacuum systems to accept a Fulbright Scholarship to Purdue University, where he obtained a master's degree. Returning to TUM he finished his thesis and married. Hillenkamp's first job was with the Federal Department of Science and Technology, where he taught himself lasers and worked with them for fourteen years. During this time he also got his PhD, writing his thesis on energy meters for Q-switch lasers. Hillenkamp met Raimund Kaufmann and the two began a long lasting collaboration; eventually this collaboration led Hillenkamp and Michael Karas to the invention of, first, laser-induced microprobe mass analysis, or LAMMA; and then matrix-assisted laser desorption ionization, or MALDI, which has been profoundly important in biology.

Researching the safety of lasers led Hillenkamp to found a laser-tissue interaction laboratory; this lab became the prototype for the Wellman Center for Photomedicine at Massachusetts General Hospital. Hillenkamp held a position at J. W. Goethe Universiẗt in Frankfurt before moving to the University of Münster, where he became chair and Director of the Department of Medical Physics and Biophysics. At that time Münster was considered the center of mass spectrometry in Germany. Hillenkamp has also held visiting positions at Harvard Medical School, Massachusetts General Hospital, Universitá degli Studi di Napoli, University of Maryland in Munich, and other places. He helped develop a submission for the Excellence Initiative before he retired.