A suite of perfluoroalkyl substances (PFASs) and polychlorinated naphthalenes (PCNs) were determined in 41 peregrine falcon eggs collected in South Greenland between 1986 and 2014. Median concentrations of perfluorinated sulfonic acids (ΣPFSA) and perfluorinated carboxylic acids (ΣPFCA) were 303 ng/g dry weight (dw) (58 ng/g wet weight, ww) and 100 ng/g dw (19 ng/g ww), respectively, which was comparable to other studies. Perfluorooctane sulfonate (PFOS) accounted for 94% on average of all PFSAs, but did not show a significant time trend. Perfluorohexane sulfonate (PFHxS), perfluoroheptane sulfonate (PFHpS) and perfluorodecane sulfonate (PFDS) showed non-linear decreases over the study period, while some long-chain PFCAs increased significantly. The PCN profile was dominated by the penta-, hexa- and tetrachlorinated congeners CN-52/60, CN-66/67 and CN-42. CN-54, an indicator of combustion, accounted for 2.4% of ΣPCN on average. All PCN congeners showed a decreasing tendency, which was significant for lipid-normalized concentrations of CN-53, CN-54 and CN-63. The ΣPCN median concentration was 21 ng/g lipid weight, which is in the high end of concentrations reported for bird eggs. The PCN and PFAS concentrations add to an already high contaminant burden and a complex chemical cocktail in the peregrine falcon population in Greenland, mainly reflecting contaminant exposure during migration and winter stays in Central and South America.