Microgeodic disease is a disease of unknown etiology that affects the fingers and toes of children, with ≥ 90% of cases involving the fingers alone. We present a rare case of microgeodic disease affecting an index finger and two toes simultaneously in a 7-year-old girl. X-ray and magnetic resonance imaging (MRI) showed multiple small areas of osteolysis in the middle phalanges of the left index finger, hallux, and second toe. Microgeodic disease was diagnosed from X-ray and MRI findings, and conservative therapy involving rest and avoidance of cold stimuli was provided. Although pathological fractures occurred in the course of conservative treatment, the affected finger healed under splinting without any deformity of the finger.