Lipschütz ulcer is an uncommon entity that is clinically characterised by a flu-like syndrome accompanied by an acute painful necrotic vulvar ulcer. It typically occurs in young women with no sexual contact history, and it is very rare among children. The aetiology is unknown, although recently several reports have related Epstein-Barr virus primary infection with this entity. We report a 17-month-old girl with fever and an acute genital ulcer. All the complementary tests for the most frequent causes of vulvar ulcers yielded negative results, whereas viral serology and polymerase chain reaction technique confirmed the presence of an acute Epstein-Barr virus infection. When main causes of genital ulcer have been excluded, and there is no history of sexual contact, Lipschütz ulcer should be included in the differential diagnosis. Detection of Epstein-Barr virus genome by polymerase chain reaction can lead to an earlier diagnosis.