The NASA Radiation Dosimetry Experiment (RaD‐X) stratospheric balloon flight mission, launched on 25 September 2015, provided dosimetric measurements above the Pfotzer maximum. The goal of taking these measurements is to improve aviation radiation models by providing a characterization of cosmic ray primaries, which are the source of radiation exposure at aviation altitudes. The RaD‐X science payload consists of four instruments. The main science instrument is a tissue‐equivalent proportional counter (TEPC). The other instruments consisted of three solid state silicon dosimeters: Liulin, Teledyne total ionizing dose (TID) and RaySure detectors. The instruments were housed in an aluminum structure protected by a foam cover. The structure partially shielded the detectors from cosmic rays but also created secondary particles, modifying the ambient radiation environment observed by the instruments. Therefore, it is necessary to account for the influence of the payload structure on the measured doses. In this paper, we present the results of modeling the effect of the balloon payload on the radiation detector measurements using a Geant‐4 (GEometry ANd Tracking) application. Payload structure correction factors derived for the TEPC, Liulin, and TID instruments are provided as a function of altitude. Overall, the payload corrections are no more than a 7% effect on the radiation environment measurements.