He studied at the University of Tübingen from 1908, and received his doctorate in 1912, under Friedrich Paschen. The subject of his dissertation was on the measurement of radiation. After obtaining his doctorate, he continued on as an assistant to Paschen, which he had been since 1911. Gerlach completed his Habilitation at Tübingen in 1916, while serving during World War I.
Gerlach became a Privatdozent at the University of Tübingen in 1916. A year later, he became a Privatdozent at the Georg-August University of Göttingen. From 1919 to 1920, he was the head of a physics laboratory of Farbenfabriken Elberfeld, formerly Bayer-Werke.
In 1925, Gerlach took a call and became an ordinarius professor at the University of Tübingen, successor to Friedrich Paschen. In 1929, he took a call and became ordinarius professor at the Ludwig Maximilians University of Munich, successor to Wilhelm Wien. He held this position until May 1945, when he was arrested by the American and British Armed Forces.
From 1937 until 1945, Gerlach was a member of the supervisory board of the Kaiser-Wilhelm-Gesellschaft (KWG). After 1946, he continued to be an influential official in its successor organization after World War II, the Max-Planck-Gesellschaft (MPG).
On 1 January 1944, Gerlach officially became head of the physics section of the Reichsforschungsrat (RFR, Reich Research Council) and Bevollmächtigter (plenipotentiary) of nuclear physics, replacing Abraham Esau. In April of that year, he founded the Reichsberichte für Physik, which were official reports appearing as supplements to the Physikalische Zeitschrift.
From May 1945, Gerlach was interned in France and Belgium by British and American Armed Forces under Operation Alsos. From July of that year to January 1946, he was interned in England at Farm Hall under Operation Epsilon, which interned 10 German Scientists who were thought to have participated in the development of atomic weapons.
Upon Gerlach's return to Germany in 1946, he became a visiting professor at the University of Bonn. From 1948, he became an ordinarius professor of experimental physics and Director of the physics department at the University of Munich, a position he held until 1957. He was also rector of the university from 1948 to 1951.
From 1949 to 1951, Gerlach was the founding President of the Fraunhofer-Gesellschaft, which promotes applied sciences. From 1949 to 1961, he was the vice-president of the Deutsche Gemeinschaft zur Erhaltung und Förderung der Forschung (German Association for the Support and Advancement of Scientific Research); also known in short as the Deutsche Forschungs-Gemeinschaft (DFG), previously the Notgemeinschaft der Deutschen Wissenschaft.
In 1957, Gerlach was a co-signer of the Göttingen Manifesto, which was against rearming the Federal Republic of Germany with atomic weapons.