A fledgling feral pigeon with systemic protozoal infection was referred with corneal protrusion in the right eye after being treated for a corneal ulcer for 12 days. Ophthalmic examination revealed a corneal bulla covering almost the entire central cornea and preventing the eyelids from closing. Gelatinous corneal stroma with numerous heterophils surrounding the corneal bulla was also detected on cytologic examination. Bullous keratopathy and melting keratitis in the right eye were diagnosed. Temporary tarsorrhaphy with topical eye drops was prescribed for a week; however, the bulla persisted. A modified nictitating membrane flap was created under general anesthesia and maintained for 2 weeks. The corneal bulla resolved, and corneal thickness was restored. The pigeon was presented again with recurrence of the corneal bulla in the right eye after 45 days. Alternative surgical options were recommended; however, the pigeon was euthanized because the protozoa‐induced intra‐oral and intra‐aural masses caused malformation of the beaks, which made voluntary feeding impossible.