For significant contribution in the field, in 1991 he was awarded, along with Bert Sakmann, the Nobel Prize in Physiology or Medicine for "their discoveries concerning the function of single ion channels in cells".

While at the Charles Stevens Laboratory at Yale University for post-doctoral work he met fellow scientist Eva-Maria Neher, whom he married in 1978 and subsequently the couple had five children – Richard, Benjamin, Carola, Sigmund, and Margret.

In 1987, he received the Gottfried Wilhelm Leibniz Prize of the Deutsche Forschungsgemeinschaft, which is the highest honour awarded in German research.

Along with Bert Sakmann, he was awarded the Nobel Prize in Physiology or Medicine in 1991 for "their discoveries concerning the function of single ion channels in cells".

[12] Neher and Sakmann were the first to record the currents of single ion channels on a live cell (they were first recorded using the lipid bilayer method) through their development of the patch-clamp technique,[13][14][15][16] a project Neher began as a postdoctoral research associate in the laboratory of Charles F. Stevens at Yale.