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James Harvey Wilbur was born in Lowville, New York on September 11, 1811. He married Lucretia Anne Stevens on March 9, 1831, and soon after they converted to Methodism at a camp revival meeting. Wilbur was admitted on trial to the Black River Conference of the Methodist Episcopal Church the following year and served as a circuit-riding missionary in upstate New York until he received a letter on September 26, 1846 calling him to the Oregon Mission. A month later Wilbur and his family sailed on the ship Whiton to the Oregon Territories. Wilbur documented this trip in his journal. A published version of the journal is titled "Travels of J. H. Wilbur: Journal written from September 27, 1846 to January 25, 1848 from New York around Cape Horn to the Oregon Institute and the onset of his Methodist mission work in Oregon Territory."

Upon arriving in Oregon, Wilbur traveled to the Willamette Valley where he became principal of the Oregon Institute, predecessor of Willamette University, in 1848. For the next two years, Wilbur; his wife; and daughter, Ann, taught at the school.

After his term at the Oregon Institute ended in 1850, Wilbur was assigned to the Oregon City and Columbia district, centered in Portland, where he worked making real estate investments for himself and the Methodist conference. In 1851 and 1852, Wilbur helped to purchase land, raise funds, and build the first Methodist church in the city, Taylor Street Methodist Church, as well as the Portland Academy and Female Institute, a secondary school similar to the Oregon Institute. In 1853 Wilbur was assigned to the Umpqua River Valley district in southern Oregon where he founded the secondary school, Umpqua Academy (later known as Wilbur Academy). Wilbur served in this district until 1857.

After two years, 1857 to 1859, as a substitute teacher at Willamette University, Wilbur was reassigned to the Columbia River district, encompassing Portland, The Dalles, and Walla Walla in the Washington Territory. During a tour of his new circuit-riding territory in the summer of 1859, Wilbur visited Fort Simcoe and the Yakama Indian Agency for the first time. Following a series of discussions about the potential for education on the reservation, Wilbur accepted the new position of Superintendent of Instruction, and he and Lucretia moved to the Yakama Indian Agency in the fall of 1860. Wilbur improved the educational program at the fort but difficulties with staff and fellow agents in the area, including Agent A. A. Bancroft, led to Wilbur's dismissal by Superintendent B. F. Kendall in late 1861. He was reinstated, but problems at the agency sent Wilbur to Washington, D.C. to speak with President Lincoln about the situation. In June, 1864 President Lincoln appointed Wilbur to the position of Yakama Indian Agent.

The agency school operated at capacity level during Wilbur's time there. To give the Yakamas practical experience, an emphasis was placed on trade skills as well as the "four R's" (reading, writing, arithmetic, and religion). Wilbur followed a policy of distributing government annuity goods to those Yakamas who worked on the reservation (unless physically incapable of doing so), concentrating efforts on the farming of grain and care for the agency's huge herd of cattle. Some Yakama tribes rebuked Wilbur's attempts to "civilize" their people, but the Yakama Reservation became a thriving Indian agency during this time.

Despite the Yakama Agency's prosperity, there were difficulties during Wilbur's tenure as Indian Agent there. In 1869 Wilbur was dismissed as agent due to a change in policy that called for all agents to be military men. He was replaced by Lieutenant James Smith. The next year, when Congress passed legislation forbidding active military men to serve in a civilian capacity, the Wilburs returned to Fort Simcoe and resumed their duties.

Wilbur's last years as an Indian Agent covered a difficult period. War with the Nez Perce broke out in 1877. The following summer, the deaths of two white settlers resulted in the wrongful arrest of Chief Moses, chief of the Sinkiuse-Columbia tribe, whom Wilbur bailed out of jail and kept at Fort Simcoe for his own protection. In the winter of 1879, as a result of the Bannock War in which Paiutes had participated, the United States army was ordered to remove members of the Paiute tribes to the Yakama Indian Reservation. Wilbur later remarked that the newly arrived Paiute were "utterly destitute" and that he was given no notice of their coming "and of course no arrangements for giving them rations." Wilbur made emergency preparations for food, shelter, and clothing for approximately 500 people including Sarah Winnemucca, the English-educated daughter and granddaughter of Paiute chiefs.

In the fall of 1880, Wilbur took a leave of absence from his duties at the agency in order to travel to the East coast with his wife. The Wilburs planned to visit family and friends in New York and stop in Washington, D.C. to accelerate the process of auditing, balancing, and closing lapsed government bonds (the source of the agency's finances). Lucretia became dangerously ill, however, and a 60-day leave stretched into several additional months. While they were away, Indian Inspector William J. Pollock arrived to examine Fort Simcoe and spent the better part of three months there reordering the management of the fort.

After their return to Fort Simcoe, Wilbur attempted to return the fort to the management style he had set up before leaving in 1880. After assisting the Paiutes in moving their possessions from the defunct Malheur Agency to Fort Simcoe during the summer of 1881, he tendered his resignation to the Commissioner of Indian Affairs in June 1882.

The Wilburs spent their post-retirement years in Walla Walla, where Wilbur continued missionary work and real estate investments. When both he and Lucretia passed away in October of 1887, the Wilbur estate was donated to charitable causes, including a bequest to Willamette University's endowment fund.