Born in Boston, Massachusetts, Pickering graduated from Harvard in 1865. He taught physics at the Massachusetts Institute of Technology before becoming professor of astronomy and director of the observatory at Harvard in 1876, remaining there until his death in 1919.

Pickering made innovations in spectrography. Instead of placing a small prism at the focus to capture the light of a single star, he put a large prism in front of the objective, obtaining at the same time a spectrogram of all the stars in the field sufficiently bright to affect the emulsion. This made possible the massive surveys he wanted to organize and enabled the publication in 1918 of the Henry Draper Catalogue, compiled by Annie Cannon, giving the spectral types of 225,300 stars. The other innovation in instruments due to him was the meridian photometer introduced in 1880. In this, images of stars near the meridian would be reflected at the same time as the image of Polaris. The brightness could then be equalized and as the brightness of Polaris was known, that of the meridian stars could easily be calculated. More than a million observations with such instruments permitted the compilation of the Harvard catalog giving the magnitude of some 50,000 stars. He was able to include stars of the southern hemisphere in this catalog, for in 1891 he had established an observatory in Arequipa, Peru, with the help of his brother William Henry Pickering.

One further improvement due to Edward Pickering was his introduction, around 1900, of the alphabetic system of spectral classes.