John W. Gunnison was born in Goshen, New Hampshire in 1812; he graduated from West Point in 1837, second in his class of fifty cadets. After he had served one year in the Florida campaign against the Seminole Indians, his health led him to ask for a reassignment to the Corps of Topographical Engineers, where he spent the rest of his military career. But his new appointment did not take him out of the Florida swamps for another year; in 1839 he helped to build a road in Florida until his superiors were forced to send him to Saratoga Springs in order that he could recover his health. He then finished his southern tour of duty in supervising the construction of a canal in Georgia. While there, he married Martha A. Delony on 15 April 1841.

For the next eight years, 1841 to 1849, he was engaged in survey work in the Great Lakes region. He helped plot the boundary between Wisconsin and Michigan, the western coast of Lake Michigan, the coasts of Lake Erie, and the marshy areas of northern Ohio. He was promoted to the rank of first lieutenant on 9 May 1846 but did not serve in the Mexican War, continuing with his duties as an engineer in the Great Lakes area.

In the spring of 1849 he was assigned as second in command of the Howard Stansbury Expedition to explore and survey the Valley of the Great Salt Lake. During the trip across the plains in the spring and summer of that year, Gunnison was so ill that he was forced to ride in a closed carriage until, at Fort Bridger, he had recovered sufficiently to take charge of the party the rest of the way to the Mormon capital while Stansbury reconnoitered a new road to Salt Lake City. Lieutenant Gunnison spent the fall of 1849 in a survey of Utah Lake and the Jordan River, with the help of Mormon scientist Albert Carrington. During the winter spent in the city of the Saints, Gunnison made a study of the religion and culture of his hosts which later found publication as a book, The Mormons, a remarkably fair and balanced view for the time.

After the spring and summer of 1850 spent in the survey and mapping of the Great Salt Lake, the Stansbury party retraced its route back across the continent to St. Louis and, by the first part of January 1851, Captain Stansbury, Lieutenant Gunnison, and Albert Carrington were in Washington, D.C., where they spent the next five months preparing the maps and records for the publication of the Stansbury Report. Following this assignment, Gunnison was returned to the Great Lakes survey team where he spent the next two years, 1852 and 1853, in mapping the Green Bay area. He was promoted to captain on 3 March 1853.

Two months later, on 3 May, he received orders to take charge of one of the expeditions for the survey of a Pacific railroad route. He was to direct his party across the Rocky Mountains via the Herfano River, through Cochetopa Pass, and by way of the present Gunnison and Green rivers to the Sevier River. With Lieutenant E. G. Beckwith as assistant commander, the party left St. Louis on 9 June 1853 and, after an uneventful trip, by 18 October was at Manti, Utah Territory.

Then, in what was to become a tragic and controversial incident in western history, Captain Gunnison and eleven of his party encamped near the Sevier River were attacked by a band of Pahvant Indians on 26 October 1853. Only four of the men escaped, the bodies of Gunnison and the other six men being horribly mutilated by the Indians. Despite cries of outrage by some easterners that the Mormons had instigated the attack, Lieutenant Beckwith concluded, as a result of his investigation, that the Mormons were not involved and that the Pahvant Indians had acted in revenge for an earlier attack upon their people by a party of white emigrants. In extolling the career of Captain Gunnison, the Secretary of War especially emphasized his professional skill and sound judgment. Lieutenant Beckwith completed the survey that Captain Gunnison had begun.