Fischer, the son of a chemicals industrialist from Höchst-am-Main in Germany, gained his doctorate in chemistry at the University of Marburg in 1904. He also studied medicine at the University of Munich, gaining his MD in 1908. He was assistant to Emil Fischer before occupying chairs of medical chemistry at Innsbruck (1916) and Vienna (1918). In 1921 he succeeded Heinrich Wieland as professor at the Technical Institute in Munich.

Fischer's life work was the study of the immensely important biological molecules hemoglobin, chlorophyll, and the bile pigments, especially bilirubin. He showed that hemin – the nonprotein, iron-containing portion of the hemoglobin molecule – consists of a system of four pyrrole rings, linked by bridges, with iron in the center. He synthesized hemin in 1929 and extensively investigated similar molecules – the porphyrins. He was awarded the Nobel Prize for chemistry for this work in 1930. He then turned to the chlorophylls and showed that they are substituted porphins with magnesium rather than iron in the center. The bile acids were shown by Fischer to be degraded porphins, and he synthesized bilirubin in 1944. Fischer took his own life at the end of World War II, after his laboratories had been destroyed in the bombing of Munich.