We report the case of a two and a half-year-old girl who presented with injury to the right thigh along with a discharging sinus in the midthigh region following a nonorthopaedic surgical procedure. Radiographs of the thigh indicated osteomyelitis of the femoral diaphysis with pathological fracture. During follow-up examination, shortening was observed in the affected limb, along with complete separation of the femoral epiphysis with partial resorption of the femoral head. A few cases of physeal separation of the femoral head following osteomyelitis of the femoral diaphysis have been reported in the published literature, but still it may go undiagnosed until late stages because of the lack of awareness among orthopaedicians about this entity. There was no history of any precipitating trauma to the hip. This case is of interest because of the difficulty in making differential diagnosis at the first evaluation; there was an orthopaedic misdiagnosis on the basis of the lack of complete preoperative imaging. Because of the devastating sequelae on immature skeleton including limb shortening, osteomyelitis, epiphyseal separation of proximal epiphysis and pathological fracture of shaft femur, the importance of early diagnosis, complete preoperative imaging and prompt treatment must be overemphasized.