The objective of this case report was to present the development of implantation cyst following the perforating corneal injury, the problems related to the treatment, including total surgical excision of the cyst, the secondary cataract extraction, iridoplasty and the artificial intraocular lens reposition. A patient first presented with perforating corneal injury inflicted by a piece of wood, with the iris prolapse. Primary wound management, reposition of prolapsed iris and corneal sutures were performed four days after the injury. Eight months later, the patient was rehospitalized due to an implantation iris cyst and traumatic cataract. The cyst was excised, the extracapsular cataract extraction was done and the anterior chamber lens was implanted. Postoperative visual acuity was normal. Three years later, the patient presented for a follow-up examination, with the cyst filled up again, occupying two thirds of the anterior chamber. This time, the cyst was completely excised, all fibrous remnants of the secondary cataract were removed, and the iridoplasty was necessary due to large iris coloboma. Reposition of the anterior chamber lens was carried out. Histological examination revealed an implantation iris cyst covered by multilayered squamous epithelium. Normal visual acuity was achieved. The patient has been followed-up for six months uneventfully. Management of perforating corneal wound with iris prolapse may lead to development of an implantation iris cyst. Puncture of the cyst as well as incomplete excision will not solve the problem. Complete surgical removal of the iris cyst is the treatment of choice.