When developing a stratospheric balloon mission, the Thermal Control Subsystem (TCS) plays an important role for a successful mission. From a thermal point of view, in this kind of flights the payload faces extreme environmental conditions very similar to the ones found by spacecrafts. At float altitude, radiation dominates heat exchanges with the environment because convection effects can be considered neglectable. Because of that, thermal analyses are usually performed in a similar way, dimensioning the TCS for a hot and cold extreme cases in steady-state conditions. Thus, ESATAN-TMS, as the standard tool of the European Space Agency (ESA) for thermal analysis of space systems, seems an appropriate tool for stratospheric balloons thermal analyses. Nevertheless, there are some particularities during the ascent phase of this kind of missions that make the ESATAN-TMS implementation a challenge to overcome. Indeed, the changing environmental conditions, the convective effects and the variable geometry of the balloon skin are some of the main difficulties. A complete thermal analysis of a stratospheric balloon has been performed in ESATAN-TMS, in the context of SUNRISE-3 mission. Such analysis includes not only the traditional worst case scenarios, but also a full transient ascent phase thermal analysis, all based in real Earth observation data.