This dataset contains concentrations of perfluoroalkyl substances (PFAS) measured in the eggs of brown pelicans nesting near Charleston, SC, USA, as well as movements of brown pelicans tracked with GPS-Platform Terminal transmitters. In total, 36 eggs were measured from three breeding colonies of brown pelicans for the presence of 24 PFAS analytes using LC-MS/MS. Concentrations were then analyzed for differences between colonies based on urban habitat use and distance from Charleston.