X-rays and the electron were discovered consecutively in the late 19th century, with an electron lens theory introduced at the end of the 1920s. The development of higher resolution microscopes in the early 20th century is a result of using these short wavelength beams as the light source. The transmission electron microscope (TEM) was invented by Ernst Ruska of Germany in the early 1930s, and the first commercial TEM was developed by Siemens in 1939. The development of the scanning electron microscope (SEM) started around the same time as that of the TEM. Next, was the scanning transmission electron microscope (STEM), which was developed by Manfred Ardenne in the late 1930s, followed by the development of the prototype of the modern SEM by Vladimir Zworykin in the early 1940s. Zworykin's SEM, however, had a low resolution, so SEM development continued through projects at Charles Oatley's laboratory at the University of Cambridge in the 1950s, leading to the first commercial SEM produced by Cambridge Instruments in 1965.

Electron microscopes surpassed the limitations of optical microscopes and dramatically improved the resolution so that it is possible to observe objects as tiny as an atom.

In addition to improvements in resolution, many enhancements are still being made to the electron microscope. One is the development of the environmental-scanning electron microscope which maintains the sample chamber at low vacuum for observation of samples containing moisture.