To report a case of an advanced corneoscleral epithelial cyst, healed by a spontaneous marsupialization and analyzed with in vivo confocal microscopy (IVCM). A 10-year-old boy with a corneoscleral epithelial cyst, which involved the central cornea, was evaluated using IVCM (Heidelberg Retina Tomograph II with Rostock Cornea Module). The cyst emptied through a spontaneously formed minute opening in the anterior corneal stroma. Visual acuity, which had been fluctuating between 20/100 and hand motion, reached 20/50 and remained stable after a 7 months of follow-up. IVCM revealed a moderate haze under the apparently normal anterior stroma. The invading epithelium and highly reflective spheres, which probably are accumulation of desquamated cells and/or shed mucins, were demonstrated in the midstroma and deep stroma, reaching the depth of 125 μm from the uninvolved endothelium. A spontaneous collapse and healing of a corneoscleral cyst are possible. IVCM could be useful for the diagnosis and choice of the surgical treatment in the case of a recurrence.