Implementation of the hydrogen economy for emission reduction will require storage facilities, and underground hydrogen storage (UHS) in porous media offers a readily available large‐scale option. Lack of studies on multiphase hydrogen flow in porous media is one of the several barriers for accurate predictions of UHS. This paper reports, for the first time, measurements of hysteresis in hydrogen‐water relative permeability in a sandstone core under shallow storage conditions. We use the steady state technique to measure primary drainage, imbibition and secondary drainage relative permeabilities, and extend laboratory measurements with numerical history matching and capillary pressure measurements to cover the whole mobile saturation range. We observe that gas and water relative permeabilities show strong hysteresis, and nitrogen as substitute for hydrogen in laboratory assessments should be used with care. Our results serve as calibrated input to field scale numerical modeling of hydrogen injection and withdrawal processes during porous media UHS.