Born in Stuttgart, Germany, Sakmann attended the universities of Tübingen and Munich, and gained his MD from the University of Göttingen. He became a research assistant at the Max Planck Institute of Psychiatry, Munich (1969–70), and subsequently spent two years as a British Council Fellow at the Biophysics Department of University College, London (1971–73). In 1974 he joined the Max Planck Institute for Biophysical Chemistry at the University of Göttingen, becoming head of the membrane physiology unit in 1983 and director in 1985. Two years later he was appointed professor in the department of cell physiology. In 1989 he moved to Heidelberg as director of the cell physiology department of the Max Planck Institute for Medical Research.

While working at Göttingen in the mid-1970s, in collaboration with the biophysicist Erwin Neher, Sakmann developed the so-called ‘patch-clamp’ technique for studying ion channels in cell membranes. This, together with their descriptions of the biophysical properties of the channels, earned them the 1991 Nobel Prize for physiology or medicine.