The Double Focusing Mass Spectrometer (DFMS) onboard the Rosetta spacecraft employs an electrostatic and a magnet sector for energy and mass discrimination, resulting in a high mass resolution. A built-in feedback loop uses the measured magnet temperature to compensate for the temperature dependence of the magnet’s field strength. Still, large onboard temperature variations and other effects cause any given mass peak to move over a range of 30 pixels or more on the detector during the mission. The present paper discusses the various factors that contribute to the time variations in the mass calibration relation. A technique is developed to evaluate and correct for these factors. A mass calibration relation that is valid for the DFMS neutral high mass resolution mode measurements throughout the entire mission for the mass range m/z=13–69 is established and its accuracy is evaluated. The 1σ precision turns out to be less than a single pixel, which is excellent as full peak width at half height is about 12 pixels. The proposed approach provides an a posteriori mass calibration and is useful for all magnet-based mass spectrometers where experimental mass calibration by comparison to reference species, temperature stabilization, and/or electrostatic compensation, are not possible or fail to deliver a mass scale precision that is comparable to the mass resolution of the instrument.