A coolant having a set temperature is fed into the nuclear reactor core of a medical neutron source, which is in a subcritical state. The nuclear reactor core is transitioned from the subcritical state to a critical state until the nominal power of the nuclear reactor is achieved. A neutron output channel is opened in order to conduct a neutron therapy session, and the operation of the reactor is maintained at nominal power while the neutron therapy session is conducted. At the end of the session, the neutron output channel is closed at the same time as the reactor core is transitioned to a subcritical state. The temperature of the coolant entering the core is maintained unchanged and equal to a set temperature, both when the core is transitioned to a critical state and during the operation of the nuclear reactor at nominal power.