A ganglion cyst is a cystic lesion containing myxoid matrix and lined by a pseudomembrane. A ganglion cyst arising from the infrapatellar fat pad is very rare, with only a few reports appearing in the literature, and the present case is the first report of this lesion in a child. A 10-year-old boy presented with right knee pain that showed no improvement despite resting from sports activity for 1 month. Magnetic resonance imaging revealed a multilobular mass between the infrapatellar fat pad and anterior cruciate ligament. Arthroscopic excision of the mass was performed. The mass was noted to arise from the infrapatellar fat pad and was filled with myxoid matrix. The histological diagnosis was a ganglion cyst. In active pediatric patients with pain or limited range of motion in the knee, physicians should consider the possibility of a ganglion cyst from the infrapatellar fat pad, despite its rarity.