The present invention relates to a system and method for managing the operation of a turbocharger and is responsible for controlling the turbocharger to cause a desired air mass flow to be provided to the engine and for protecting the turbocharger from excessive shaft speed and excessive turbine inlet temperature. The protection modes have higher priority than the performance control. First, turbocharger shaft speed is checked against a programmable limit, and the turbocharger is adjusted to bring the speed under control if its speed exceeds this limit. If the speed is not above the limit, the turbine inlet temperature is checked against a second programmable limit. If the turbocharger inlet temperature is above the predetermined limit, the turbocharger is adjusted to bring the inlet temperature under control. If, after either of these adjustments are made, the predetermined limits are still exceeded by the turbocharger, then the system invokes a derating of the fueling to the engine in order to protect the turbocharger. If none of the limits have been exceeded, then the system operates the turbocharger to provide the desired air mass flow to the engine in order to maximize engine performance.