The Golden Eagle (Aquila chrysaetos) has great religious importance to many indigenous North American peoples, including the Hopi Tribe and Navajo Nation of the southwestern United States. Hopi oral traditions indicate their ancestors harvested nestling Golden Eagles prior to the arrival of Europeans to the region, and this religious practice continues today. Despite contemporary conservation concern for Golden Eagles, no studies have evaluated potential negative effects of religious harvest on populations of this species. We conducted aerial and ground searches for Golden Eagle nesting territories on the Navajo Nation from 1996–2005, and monitored occupancy and reproductive rates of territories in three study areas: one area where Hopi annually harvested eaglets, and two areas without harvest. We analyzed 9 yr of data (1997–2005) using multi-season occupancy models and generalized linear mixed models to test for differences among study areas in occupancy dynamics, and production of early-season and fledging-age nestlings. We found no significant differences in probabilities of occupancy, persistence, or colonization of territories between study areas. Territories in harvest and control areas produced similar numbers of nestlings early in the season; however, significantly fewer (53%) reached fledging age in the harvested area, suggesting collection of nestlings led to locally depressed fledgling production. Given possible declining trends of Golden Eagle populations in the southwestern U.S., we recommend continued monitoring and more intensive demographic studies to better understand the effects of religious harvest on the population of Golden Eagles nesting on the Navajo Nation.