Studies have demonstrated favorable outcomes of arthroscopic decompression for ganglion cyst in the supraspinous fossa; however, little attention has been paid to the difficulty in detecting these cysts during arthroscopy. In this report, we present 2 cases in which ganglion cysts in the supraspinous fossa were undetectable during arthroscopy. The ganglion cysts were not identified in these cases during surgery despite arthroscopic decompression being performed through the area in which the cyst was expected until the suprascapular nerve was entirely exposed. After surgery, magnetic resonance imaging (MRI) confirmed the disappearance of the ganglion cyst and external rotation strength was fully improved, without shoulder pain. We emphasize here that surgeons should be aware of this difficulty when performing arthroscopic decompression of ganglion cysts in the supraspinous fossa.