We report a case of delayed emergence from anesthesia in a 37-year-old male who came for emergency laparoscopic appendicectomy. This patient is hailing from one of the endemic zones of Malaria, Orissa State in India. Two months ago he had cerebral malaria and was treated in our intensive care unit. After recovering from cerebral malaria, he presented to us for acute abdomen, and he was taken for emergency laparoscopic appendicectomy. He had delayed emergence of around 2 h to extubate from the time of completion of surgery in spite of termination of anesthetic agents. Further investigations showed to have decreased serum levels of thyroid hormones and cortisol levels in the postoperative period. The Physician promptly diagnosed the condition as hypopituitarism a known sequel of cerebral malaria. The secondary thyroid insufficiency contributing to the delayed emergence from anesthesia. We also review the pertinent literature related to this rare sequelae of cerebral malaria and its perioperative implication to the anesthesiologist.