A method and system for calibrating nuclear instrumentation of a reactor is disclosed. The system comprises a reactor configured to operate at a low power level and an external heater configured to heat the reactor to its operating temperature and maintain the reactor in a critical state. The reactor maintains its temperature at a steady state by repeating steps of reducing the heater's power and increasing the reactor's power by changing one or more reactivity settings, wherein the reduced heater's power is compensated by using the increased power generated by the reactor itself. The nuclear instrumentation is configured to measure the reactor's output power and compare it with the calculated reactor's power. Based on the discrepancy between the calculated power and the measured power exceeds a threshold; and the nuclear instrumentation is appropriately calibrated by adjusting one or more settings.