Moorehead was based at the Phillips Academy, Andover, MA, from 1901-1938. He and Evelyn had a second son, Singleton Peabody Moorehead, who would become a key architect with the Colonial Williamsburg Foundation and is buried on the grounds of Bruton Parish Church there. With Peabody's influence and money, a museum and program was established at Phillips Andover Academy, with the dedication program including a fellowship from the Peabody-established Victoria Institute and the award of an honorary doctorate from Dartmouth College (also a recipient of significant Peabody largesse). He was also Curator of the University Museum of Ohio State University (1894–1897), worked at archaeological sites along the Ohio River, and at Chaco Canyon and up into Mesa Verde. As head of the Robert S. Peabody Museum of Archaeology in Andover, Massachusetts from 1902 to 1920, Moorehead launched into a program of research and publication that went on to include the Red Paint People of the Atlantic coast, Cahokia Mounds in Illinois from 1921, and Etowah Indian Mounds in Georgia from 1925. His approach was not without detractors. In 1923, the fledgling Central Section of the American Anthropological Association sent him a rebuke concerning a flyer he had distributed which had laid out a manner in which collectors of artifacts could cooperate with him or other archaeologists. Moorehead worked at the Cahokia site between 1921-1927. Cahokia is now a UNESCO World Heritage site. He was instrumental in getting the State of Illinois to buy a portion of the Cahokia site in order to create a state park. From 1927 to 1939 he worked on sites in the Illinois River Valley. Major collections from Cahokia are at the Illinois State Museum and the University of Illinois (). In the 1920s Moorehead excavated the Von Mach Site on the property of Edmund von Mach in Brooksville, Maine. The site was added to the National Register of Historic Places on January 17, 1989. Moorehead began excavation at the Etowah mounds site in Georgia during the winter of 1925. His work lasted four winter seasons, conducting excavations on Mound C and the surrounding village area. Moorehead's work on Mound C led to the discovery of a rich array of Mississippian culture goods. While working on Mound C, Moorehead also worked a small amount on Mounds A and B, but his excavation was object-oriented and ceased soon after no exotic goods were encountered. The "Etowah Papers", Moorehead's report, were published in 1932.