Jupiter's upper atmosphere is ∼700 K hotter than predicted based on solar extreme ultraviolet heating alone. The reason for this still remains a mystery and is known as the “energy crisis.” It is thought that the interaction between Jupiter and its dynamic magnetosphere plays a vital role in heating its atmosphere to the observed temperatures. Here, we present a new model of Jupiter's magnetosphere‐ionosphere‐thermosphere‐coupled system where we couple a three‐dimensional atmospheric general circulation model to an axisymmetric magnetosphere model. We find that the model temperatures are on average ∼60 K, with a maximum of ∼200 K, hotter than the model's two‐dimensional predecessor making our high‐latitude temperatures comparable to the lower limit of observations. Stronger meridional winds now transport more heat from the auroral region to the equator increasing the equatorial temperatures. However, despite this increase, the modeled equatorial temperatures are still hundreds of kelvins colder than observed. We use this model as an intermediate step toward a three‐dimensional atmospheric model coupled to a realistic magnetosphere model with zonal and radial variation.