Disclosed is a system and method for calibrating a magnetometer of a compass. With a global navigation satellite system receiver, a current position is determined. The determined position is used to determine a magnetic inclination (e.g., by a global magnetic field model such as the World Magnetic Model). The calibration system may perform different calibration sequences based on the magnetic inclination. In a first calibration sequence, performed responsive to a determination that a magnetic inclination (or the absolute value of the magnetic inclination) is less than a threshold, magnetic field data is measured by the magnetometer as it is rotated through horizontal rotation paths. If the magnetic inclination is greater than the threshold, magnetic field data is measured by the magnetometer as it is rotated through vertical rotation paths. The measured magnetic field data may be used to determine calibration values for the magnetometer compass.