Fibropapillomatosis (FP) has a complex etiology, involving genetic and environmental factors, and is considered a threat to green sea turtles (Chelonia mydas). The goals of this study were to evaluate phagocytosis and oxidative burst in blood samples of green sea turtles with and without FP. We analyzed samples from 38 specimens (27 with FP) captured at a feeding area in Brazil. No differences were observed between specimens with and without FP regarding leukocyte activity; nevertheless, the analyses revealed there were significant differences among leukocyte populations of animals with FP, lymphocytes and monocytes had higher phagocytic activity than did granulocytes, and lymphocytes had lower oxidative burst activity than did granulocytes and monocytes. This study described an efficient method to assess leukocyte activity through flow cytometry and revealed important characteristics of white blood cells from green sea turtles with FP.