Sakmann was born in Stuttgart, the son of Annemarie (née Schaefer), a physical therapist, and Bertold Sakmann, a theater director.[7] Sakmann enrolled in Volksschule in Lindau, and completed the Wagenburg gymnasium in Stuttgart in 1961. He studied medicine from 1967 onwards in Tübingen, Freiburg, Berlin, Paris and Munich. After completing his medical exams at Ludwig-Maximilians University in Munich, he became a medical assistant in 1968 at Munich University, while also working as a scientific assistant (Wissenschaftlicher Assistent) at Munich's Max-Planck-Institut für Psychiatrie, in the Neurophysiology Department under Otto Detlev Creutzfeldt. In 1971 he moved to University College London, where he worked in the Department of Biophysics under Bernard Katz. In 1974, he completed his medical dissertation, under the title Elektrophysiologie der neuralen Helladaptation in der Katzenretina (Electrophysiology of Neural Light Adaption in the Cat Retina) in the Medical Faculty of Göttingen University.[3]
Afterwards (still in 1974), Sakmann returned to the lab of Otto Creutzfeldt, who had meanwhile moved to the Max Planck Institute for Biophysical Chemistry in Göttingen. Sakmann joined the membrane biology group in 1979.
In 1990 he accepted a position at the Faculty of Natural Science Medicine at Heidelberg University. One year later, he became a full university professor at the Faculty of Biology in Heidelberg.
On 2 June 2009, Peter Gruss, the president of the Max Planck Society, announced that Sakmann would serve as the scientific director of the Max Planck Florida Institute, the organization's biomedical research facility at Florida Atlantic University in Jupiter, Florida.
Sakmann is the founder of the Bert-Sakmann-Stiftung.