Born in Munich in Bavaria, Boehm learned his father's trade of goldsmithing. After making his own flute, he quickly became proficient enough to play in an orchestra at the age of eighteen and at twenty-one he was first flautist in the Royal Bavarian Orchestra. Meanwhile, he experimented with constructing flutes out of many different materials—tropical hardwoods (usually Grenadilla wood), silver, gold, nickel and copper—and with changing the positions of the flute's tone holes.
After studying acoustics at the University of Munich, he began experimenting on improving the flute in 1832, first patenting his new fingering system in 1847. He published Über den Flötenbau ("On the construction of flutes"), also in 1847. His new flute was first displayed in 1851 at the London Exhibition. In 1871 Boehm published Die Flöte und das Flötenspiel ("The Flute and Flute-Playing"), a treatise on the acoustical, technical and artistic characteristics of the Boehm system flute. Some of the flutes he made still function. His fingering system has also been adapted to other instruments, such as the oboe and the clarinet.