Perineal endometriosis is a rare disease characterized by the presence of ectopic endometrial stroma and glands in the perineum. Most commonly observed in the episiotomy scar after normal vaginal deliveries, perineal endometriosis is not often considered in the differential diagnosis of perineal masses. This could lead to unnecessary investigations and inadequate patient treatments. Scar endometriosis is an infrequent type of extrapelvic endometriosis. Scar endometriosis can be a diagnostic challenge in Fine needle aspiration cytology (FNAC) smears that at times, is the first diagnostic modality in some cases. The challenge is amplified when the clinical details are limited and cytopathological features reveal nuclear atypia.