Joseph Schafer was Oregon's first academically trained, professional historian, serving on the faculty of the University of Oregon for twenty years. While in Eugene, he wrote what became a classic textbook on Pacific Northwest history. A student of Frederick Jackson Turner’s at the University of Wisconsin, Schafer remained a defender of Turner's famous "frontier thesis" of American history—which ascribed the nation's profoundly democratic, innovative, and individualistic tendencies to the frontier experience—long after many historians had turned against it.

Born in 1867 on a farm near Muscoda, Wisconsin, Schafer was the son of German immigrant parents. The progressive political and social views of his father, Mathias Schafer, a schoolteacher and a relatively prosperous farmer, helped shape Joseph’s views on history, politics, and society. He obtained a teaching certificate in 1889 from Madison Normal School in Dakota Territory (now South Dakota) and taught high school for two years before enrolling as a junior at the University of Wisconsin in Madison in 1892. He received a bachelor’s degree in 1894 and began his graduate studies with Frederick Jackson Turner as his advisor and mentor. He married Lily Abbott in 1895; they would have six children.

With work on his doctorate completed except for finishing the dissertation, Schafer accepted a teaching position at the University of Oregon in 1900. On his way west, in order to gain a better sense of the experiences of Oregon-bound emigrants during the 1840s-1850s, Schafer and a friend bicycled from Omaha, Nebraska, along the South Platte River to Cheyenne, Wyoming. He would receive his PhD from the University of Wisconsin in 1906.

In Eugene, Schafer played an important role in university president Prince Lucien Campbell's campaign to enhance the institution's professional reputation. While teaching courses, Schafer’s output of books was prodigious, and his scores of articles appeared in such venues as the Journal of the Mississippi Valley Historical Association, Agricultural History, Oregon Historical Quarterly, and the Wisconsin Magazine of History.

A true Progressive, Schafer worked to improve Oregon's public schools through providing methods forbetter training of teachers, and he participated in Rural Life uplift projects—Progressive-era efforts to enrich the cultural life and broaden the knowledge of rural residents—by giving lectures in small communities across the state. Inspired by Wisconsin's success in the endeavor, he was prominent in Oregon's "free library" movement.

A History of the Pacific Northwest, which Schafer published in 1905 and revised in 1918, set a new standard for the region, far surpassing in conceptual sophistication the nineteenth-century state histories of the West published by H.H. Bancroft and others. Instead of producing a narrative defined by political boundaries, he took a broader, regional view. He considered the Northwest's most recent decades, including the development of transportation, agriculture, and industry, as well as social-political trends. In the 1918 edition, for example, Schafer wrote that although "the populations of Northwest cities" were "less complex" than those of large eastern and midwestern cities, "in them one still found the deep social rift between the 'masses' and the 'classes' which constitutes the special problem of American democracy."

Neither a paean to hardy American pioneers nor a muckraking exposé of their failings, the book marked the historiographical maturity of the Pacific Northwest. A History of the Pacific Northwest was reprinted many times and was the region's basic history text into the 1950s, when it was replaced by Empire of the Columbia, by Dorothy O. Johansen and Charles M. Gates.

In 1920, the State Historical Society of Wisconsin lured Schafer back to Madison to serve as its superintendent and editor of the Wisconsin Magazine of History. He focused his energy on an ambitious project, the Wisconsin Domesday Book, a series of fine-grained studies of the state's farming and mining locales.

Schafer joined the debate on the American frontier as a supposed "safety valve" that prevented labor strife. He wrote a biography of statesman and political reformer Carl Schurz, and his Social History of American Agriculture became a classic in the field. He served as president of the Mississippi Valley Historical Society (now the Organization of American Historians) and the Agricultural History Society. In politics, Schafer was an internationalist, an anti-imperialist, and, according to his colleague John D. Hicks, a "consistent liberal who spoke out fearlessly in defense of his views."

With some of his children living in Oregon, Schafer returned twice to Eugene to teach summer courses. The University of Oregon awarded him an honorary L.L.D. degree in 1933. Schafer died on January 27, 1941. Alfred Powers, writing in the Oregon Historical Quarterly, remembered that half of Schafer's "mature, creative, productive life—the magnificent, buoyant tireless first half—was given to Oregon."