Fibropapillomatosis (FP) can be an important conservation threat to green sea turtles (Chelonia mydas) due to its widespread distribution and complex aetiology. Thus, understanding the impacts of FP in sea turtle populations is a research priority towards conservation efforts. The body condition index (BCI), based on straight carapace length (SCL) and body mass (BM), is an accurate indicator of body-nutritional condition that can be used in routine green turtle health evaluations. This study aimed to compare BCI in FP-free (N = 369) and FP-affected (N = 518) green turtles from Brazilian feeding areas. Body condition indices were evaluated in terms of the South-west Atlantic Fibropapillomatosis Score – FPSSWA (mild, moderate and severe), study sites (five Brazilian states), origin (intentional capture, fishery, stranding and afloat) and sex (when known). Curved and straight carapace lengths, and body mass were recorded in order to calculate BCI. Statistical analysis revealed significant differences in BCI among green turtles from different study areas (P = 0.02), and lower BCI values in FP-free than in FP-positive individuals (P < 0.0001). With regards to origin, the highest BCI was found in the intentional capture group (N = 245; 1.47 ± 0.16), followed by fishery (N = 180; 1.46 ± 0.20). Analysis according to sex revealed a higher mean BCI among females than males (P < 0.017). This study provides relevant data on the health and nutritional status of green turtles along the Brazilian coast, in important feeding areas for this species.