Abstract The thermospheric mass density variations and the thermosphere-ionosphere coupling during geomagnetic storms are not clear due to lack of observables and large uncertainty in the models. Although accelerometers on-board Low-Orbit-Earth (LEO) satellites can measure non-gravitational accelerations and derive thermospheric mass density variations with unprecedented details, their measurements are not always available (e.g., for the March 2013 geomagnetic storm). In order to cover accelerometer data gaps of Gravity Recovery and Climate Experiment (GRACE), we estimate thermospheric mass densities from numerical derivation of GRACE determined precise orbit ephemeris (POE) for the period 2011–2016. Our results show good correlation with accelerometer-based mass densities, and a better estimation than the NRLMSISE00 empirical model. Furthermore, we statistically analyze the differences to accelerometer-based densities, and study the March 2013 geomagnetic storm response. The thermospheric density enhancements at the polar regions on 17 March 2013 are clearly represented by POE-based measurements. Although our results show density variations better correlate with Dst and k-derived geomagnetic indices, the auroral electroject activity index AE as well as the merging electric field Em picture better agreement at high latitude for the March 2013 geomagnetic storm. On the other side, low-latitude variations are better represented with the Dst index. With the increasing resolution and accuracy of Precise Orbit Determination (POD) products and LEO satellites, the straightforward technique of determining non-gravitational accelerations and thermospheric mass densities through numerical differentiation of POE promises potentially good applications for the upper atmosphere research community.