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Simultaneous infrared observations of H3+${\mathrm{H}}_{3}^{+}$and H2emissions from Jupiter's northern aurora using the Near Infrared Spectrograph at Keck Observatory were used to measure the ionospheric and thermospheric wind velocities. H3+${\mathrm{H}}_{3}^{+}$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 H2flows, 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 H3+${\mathrm{H}}_{3}^{+}$and H2emissions 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. We observed both charged and neutral molecules in Jupiter's northern aurora from the Keck Observatory. The velocity of the charged particles shows that they are controlled by magnetic field lines that stretch into the surrounding space environment, as expected at the top of the atmosphere. However, neutrals at the top of the atmosphere also appear to be indirectly controlled by the magnetic field, driven by impacts with the ions into a large vortex that sits within Jupiter's auroral region. Because the charged and neutral molecules move differently from one another, this can drive high‐altitude currents. Charged particles flow through the neutrals in two jets, moving toward the Sun on both sides of Jupiter's aurora, driving asymmetric currents more like the system of currents that form Earth's aurora. It suggests that Jupiter has different currents closing at different altitudes in the auroral region. This layering of currents matches recent observations made by the Juno mission and may help explain some of the apparent conflicts between different Juno data sets. Our discovery also highlights the importance of interactions between charged and neutral particles on other planets, including Earth, making Jupiter an important comparator for future studies of these interactions. An aurorally aligned subcorotational thermospheric vortex is detected in Jupiter's upper atmosphereTwo sunward ionospheric jets flowing through the thermosphere are revealed on both dawn and duskJupiter potentially has a multilayer ionosphere driven separately by asymmetric currents and breakdown‐in‐corotation Pedersen currents An aurorally aligned subcorotational thermospheric vortex is detected in Jupiter's upper atmosphere Two sunward ionospheric jets flowing through the thermosphere are revealed on both dawn and dusk Jupiter potentially has a multilayer ionosphere driven separately by asymmetric currents and breakdown‐in‐corotation Pedersen currents