Introduction: Due to the increasing number of patients in need of organ transplants and the limited number of qualified brain-dead patients, it is necessary to take steps to increase the number and performance of transplantable organs of brain-dead patients through optimal compliance with scientific protocols. Methodology: In this study, two groups of 32 eligible brain-dead patients were randomly assigned to two groups. In the first group, all orders were issued by the physician and the nurses did not have the right to interfere in the diagnosis and treatment processes. However, in the second group, the trained nurses used the protocol in caring for and treating patients and sought medical help when needed. Findings: There were no clear differences in the conditions of the patients in the two groups before the intervention. However, after the intervention, the mean serum sodium, potassium, and BUN levels, the mean arterial pressure, and the cardiac index were closer to normal values and the need for vasopressors was lower in the protocol group than in the non-protocol group. However, the two groups did not differ significantly in serum creatinine and liver enzymes (ALT, AST) levels or immortality rate of brain-dead patients and transplant rejection in the first 3 months after organ donation. Discussion and Conclusion: It seems that the use of the scientific protocol in caring for brain-dead patients by trained nurses can be effective in improving the physiological conditions of patients.