Fibropapillomatosis (FP) poses a significant threat to the conservation of green sea turtles (Chelonia mydas). Polycyclic aromatic hydrocarbons-PAHs are considered mutagenic, carcinogenic and toxic, and can act as cofactor of this disease. In order to evaluate possible differences between green sea turtles with and without FP, we monitored 15 PAHs in liver samples of 44 specimens (24 with FP) captured in Brazil. We detected eight PAHs and quantified phenanthrene in all green sea turtles with FP. Specimens without FP presented lower values than the tumored ones (1.48 ng g−1 and 17.35 ng g−1, respectively; p < 0.0001). There were no significant differences between tumored and non-tumored specimens, among studied areas, or Southwest Atlantic Fibropapillomatosis Score. Even though we found higher concentrations in the liver samples of green sea turtles with FP, further studies are necessary to confirm if these pollutants are involved in the pathogenesis of the disease.