To describe the clinical and histopathologic findings of a child with congenital glaucoma who developed cystic epithelial ingrowth after goniotomy. A five-month-old boy was diagnosed with congenital glaucoma due to Axenfeld syndrome. Goniotomy was performed immediately after the clinical diagnosis in his left eye. Cystic epithelial ingrowth was noted two years postoperatively. The cyst was incompletely excised elsewhere, and recurred two years later. Cystic epithelial ingrowth expanded from the 2 o'clock to the 4 o'clock position involving the chamber angle. Best corrected preoperative visual acuity was 20/600 in his left eye. Cystic epithelial ingrowth was treated by block excision (8.0 mm) and tectonic corneoscleral grafting (8.1 mm). Best corrected postoperative visual acuity was 20/200 and the intraocular pressure was 8 mmHg without antiglaucomatous medication. There was no recurrence of the cyst during the 31 months of follow-up. Histopathologic results found that cystic epithelial ingrowth consisted of nonkeratinizing squamous epithelium with goblet cells covering Descemet's membrane, the chamber angle structures, the anterior face of the ciliary body, and the iris. Cystic epithelial ingrowth is a rare complication after goniotomy. Block excision with tectonic corneoscleral grafting is the treatment of choice for cystic and diffuse sheet-like epithelial ingrowth.