Otto Heinrich Warburg was born in Freiburg im Breisgau in 1883, close to the Swiss border. Otto's mother was the daughter of a Protestant family of bankers and civil servants from Baden. His father, Emil Warburg, had converted to Protestantism as an adult, although Emil's parents were Orthodox Jews.[4] Emil was a member of the illustrious Warburg family of Altona. Emil was also president of the Physikalische Reichsanstalt, Wirklicher Geheimer Oberregierungsrat (True Senior Privy Counselor)

Otto Warburg studied chemistry under Emil Fischer, and earned his doctorate in chemistry in Berlin in 1906. He then studied under Ludolf von Krehl and earned the degree of doctor of medicine in Heidelberg in 1911