Jupiter's magnetosphere-ionosphere-thermosphere system drives the brightest, steadiest aurora in our solar system. This emission is the result of an electrical current system, which couples the magnetosphere to the planetary atmosphere in an attempt to enforce the corotation of the middle magnetospheric plasma. Field-aligned currents transfer angular momentum from the atmosphere to the magnetosphere. In the equatorial plane, the field-aligned currents diverge into radially outward currents, which exert a torque on the plasma due to the J × B forces. Equatorward ionospheric currents exert an opposite torque on the ionosphere, which interacts with the thermosphere via ion-neutral collisions. The upward field-aligned currents result in auroral electron precipitation, depositing energy into the high-latitude atmosphere. This energy input is a possible candidate for explaining the large thermospheric temperature measured by the Galileo probe at equatorial latitudes; however, previous atmospheric circulation models have shown that the bulk of the energy is transported poleward, rather than equatorward. We present numerical results of Jupiter's coupled magnetosphere-ionosphere-thermosphere system including, for the first time, field-aligned potentials. The model is compared with three previously published works. We find that the rotational decoupling of the magnetospheric and thermospheric angular velocities in the presence of field-aligned potentials tempers the thermospheric response to the outward transport of magnetospheric plasma, but this is a secondary effect to variations in the Pedersen conductance.