In 1891 Pickering joined his brother Edward in establishing the Boyden station of the Harvard Observatory at Arequipa, Peru. He returned to the United States in 1893 and the next year erected the observatory and telescope at Flagstaff, Ariz., for the noted U.S. astronomer Percival Lowell. In 1900 he established a station for the Harvard Observatory at Mandeville.

He discovered Phoebe in 1899 and noted that it revolves around Saturn in the opposite direction (retrograde) from that of Saturn's other satellites. His announcement in 1905 of a 10th satellite, which he named Themis, is generally discounted, for it was never observed again. The 10th satellite (Janus) that was discovered in 1967 is probably not the same one, for its orbit is the innermost of all Saturn's moons, whereas Pickering's Themis was supposed to lie between Titan and Hyperion. In 1919 Pickering also predicted the existence of, and gave a position for, an object orbiting beyond Neptune. This work contributed to the discovery of Pluto.