BackgroundIntracorneal epithelial cysts are a rare clinical condition that can occur anywhere in the corneal tissue; however, they appear most commonly in the stroma. They are sometimes challenging to treat because of their location, depth, and visual outcomes. Herein, we report a pre-Descemet epithelial cyst that was successfully treated surgically, with guidance from Fourier-domain optical coherence tomography (FD-OCT).Case presentationThis interventional case report presents a patient with gradually decreasing vision caused by a pre-Descemet epithelial cyst. A 4-year-old girl with no history of trauma or ocular surgery showed a deep-seated intracorneal cyst in her left eye (8 o’clock corneoscleral area, dissecting into the pre-Descemet cornea). The cyst was threatening the visual axis. An epithelial cyst was diagnosed after drainage on the basis of the cyst contents. We irrigated inside the cyst using 10% trichloroacetic acid (TCA), distilled water, and 1% 5-fluorouracil (5-FU) solutions for chemical cyto-destruction of the lining epithelial cells of the cystic wall. We used a portable FD-OCT during operation to guide this procedure, without perforating the Descemet’s membrane and endothelial layer. Recurrence could be prevented after removal of the cystic tissue located in the sclera area outside of the limbus. No recurrence was noted during the 4-year follow-up.ConclusionWhen treating centrally deep-seated intracorneal epithelial cysts, clinicians must consider recurrence, endothelial damage, and visual outcome. Herein we report the case of a deep-seated, intracorneoscleral epithelial cyst that was completely resolved with chemical cyto-destruction and removal of the intrascleral cystic tissue under the guidance with FD-OCT; thus, endothelial damage could be minimized.