During the first International Polar Year, a joint program of scientific research sponsored by 11 nations (1882–83), Greely commanded the U.S. station at Fort Conger on northeastern Ellesmere Island. From August 1881 to August 1883 the expedition, consisting of 25 officers and men, recorded 500 observations each day on weather and tides and collected and studied samples of minerals, flora, and fauna. Discoveries made on sledge trips included Lake Hazen and Greely Fjord on the western side of Ellesmere. When a relief ship failed to arrive in early August 1883 the party abandoned Fort Conger and moved southward in small boats. Covering 500 miles (805 kilometres) in 51 days, the men landed at Bedford Pym Island in Smith Sound on October 15. There they faced a winter of 250 days with rations for 40 days and, before the ordeal was over, were reduced to eating their own leather clothing. Only Greely and six others survived.

Much of Greely's later army work involved laying communications lines in the Philippines, Alaska, and elsewhere. He was promoted to chief signal officer and brigadier general in 1887. In 1888 he helped found the American Geographical Society. His many published works include Three Years of Arctic Service (1886) and Handbook of Polar Discoveries (5th ed. 1910).