We present the first child case of pseudomembranous conjunctivitis accompanied by an extensive corneal ulcer with acute graft-versus-host disease (GVHD) after cord blood stem cell transplantation (CBSCT). The histopathology of the pseudomembrane and the ocular changes following its excision were investigated specifically. One week after the excision of pseudomembrane, the extensive corneal epithelial defects had totally disappeared. Pseudomembrane excision may be an effective method of treatment in corneal epithelial defects observed after GVHD.