An uncommon and dangerous disease with a fatality rate of more than 95% is caused by the amoeba known as Balamuthia mandrillaris. Here, we discuss the treatment of a patient who underwent a renal transplant and contracted the amoeba B. mandrillaris. The patient had a sudden onset of high fever on the 13th day after renal transplantation; on the morning of the 16th postoperative day, the patient's condition worsened and he was transferred to the ICU for treatment; on the 17th postoperative day, the patient was given mechanical ventilation; and on the 20th postoperative day, he underwent a lumbar large-pool puncture, combined with intrathecal injection of the administered medication. In order to prevent further deterioration of the patient's condition, the main aspects of care for this patient included close monitoring of changes in the patient's condition and early detection of risk factors; prompt emergency care for the patient's seizures; close monitoring of the efficacy and side effects of the patient's medication; and precise medication administration; improved hemodynamic monitoring while administering CRRT to the patient, as well as performing exercises on the patient's limb and respiratory functions. On the 32nd postoperative day, a tracheotomy is performed following thorough monitoring and care. The ventilator was turned off on postoperative day 34, and a venturi mask was installed for tracheotomy-cannula-based oxygen administration. On surgical day 40, the intrathecal injections halted and the lumbar pool drainage tube was removed. On postoperative day 46, the patient was stabilized and transferred from the intensive care unit to the organ transplant unit for extra care. This study strictly complied with the Helsinki Congress and the Istanbul Declaration regarding donor source.