Green sea turtles (Chelonia mydas) with cutaneous fibropapillomatosis (FP) occur in some populations worldwide, and the survivability of these individuals may be compromised depending on the disease severity score. Furthermore, populations may be negatively affected in areas with a high prevalence of the disease. The stress responses (corticosterone, glucose, lactate, and hematocrit) to capture and handling were assessed in animals with different FP severity scores. From 18 January 2013 to 31 July 2014, 33 juvenile (sex was not determined) C. mydas were collected from the effluent of a steel mill in the state of Espírito Santo, Brazil, by casting a net from the bank of a canal in the morning. The body conditions of animals with FP scores of FP2 and FP3 were poor, which suggests that these turtles were unable to adequately feed themselves, and animals with an FP score of FP3 exhibited an impaired corticosterone response. This may compromise the fitness of animals in populations with a high incidence of advanced-stage FP.