Keratoconjunctivitis sicca (KCS) is a common complication of graft-versus-host disease (GVHD), and may lead to corneal epithelial defect and melting. In contrast, recurrent corneal calcareous degeneration and perforation is rare. A 46-year-old woman developed chronic GVHD after bone marrow transplantation for aplastic anemia. Severe KCS with corneal melting and calcium deposits were noted in the left eye. Penetrating keratoplasty was performed because of corneal perforation, but poor re-epithelialization and calcium deposition recurred. Lamellar keratectomy and amniotic membrane transplantation (AMT) were performed, but acute calcareous degeneration developed with subsequent recurrence of corneal perforation. After regraft, AMT and tarsorrhaphy, the corneal graft remained clear for 3 months. However, breakdown of the corneal epithelium occurred 3 weeks after spontaneous separation of tarsorrhaphy. Six months later, corneal perforation recurred again along with exacerbation of GVHD. Regraft was performed, but the patient refused tarsorrhaphy and AMT. Poor re-epithelialization persisted after regraft. Corneal melting with impending corneal perforation ensued. Further corneal surgery was refused and the patient chose to undergo evisceration. This case demonstrates that the ocular complications of GVHD may be severe enough to lead to corneal perforation and calcareous degeneration that is recalcitrant to medical and surgical treatment.