Baker's cyst is commonly associated with intraarticular pathology such as degenerative arthritis. Few cases of neural compression by a Baker's cyst in the popliteal fossa have been reported with intraarticular pathology. We report a case of peroneal nerve compression by an atypical Baker's cyst in a child without intraarticular pathology. A 10-year-old boy had 6-month history of the left foot drop without a known trauma. There was no swelling or pain in the knee. The electrodiagnostic study demonstrated a profound lesion of the deep peroneal nerve and a mild denervation of the superfical peroneal nerve. Magnetic resonance images displayed an atypical Baker's cyst originating from the popliteal fossa and extending to the posterolateral side of the fibular head. Clinical and electrophysiological findings improved after aspiration of the cyst.