Simultaneous infrared observations of 𝐴𝐴H+3 and H2 emissions from Jupiter's northern aurora using the Near Infrared Spectrograph at Keck Observatory were used to measure the ionospheric and thermospheric wind velocities. 𝐴𝐴H+3 ions supercorotate near the dawn auroral oval and subcorotate across the dusk sector and in the dawn polar region relative to the planetary rotation rate, broadly in agreement with past observations and models. An anticyclonic vortex is discovered in H2 flows, closely matching the mean magnetospheric subcorotation when the observed magnetospheric flows are averaged azimuthally. In comparing ion and neutral winds, we measure the line-of-sight effective ion drift in the neutral reference frame for the first time, revealing two blue-shifted sunward flows of ∼2 km/s. Observed 𝐴𝐴H+3 and H2 emissions overlap with predictions of the Pedersen conductivity layer, suggesting two different regions of the ionosphere: (a) a deep layer, where neutral forces dominate the thermosphere and symmetric breakdown-in-corotation currents can close, and (b) a higher layer, where the observed effective ion drift allows dawn-to-dusk Pedersen currents within the upper atmosphere, in turn closing asymmetric currents within the magnetosphere. This ionospheric structure aligns well with recent Juno observations of Jupiter's aurora. The detected thermospheric vortex implies the driving of neutral flows by the momentum from the magnetosphere within the thermosphere and deeper in the atmosphere to potentially 20 mbar. Jovian neutral thermosphere might bridge the gap between current observations and modelings and perhaps be significant to the dynamics of aurora on Earth and other outer planets.