We report the first observations of E region neutral wind fields and their interaction with auroral arcs at mesoscale spatial resolution during geomagnetically quiet conditions at Mawson, Antarctica. This was achieved by using a scanning Doppler imager, which can observe thermospheric neutral line-of-sight winds and temperatures simultaneously over a wide field of view. In two cases, the background E region wind field was perpendicular to an auroral arc, which when it appeared caused the wind direction within ∼50 km of the arc to rotate parallel along the arc, reverting to the background flow direction when the arc disappeared. This was observed under both westward and eastward plasma convection. The wind rotations occurred within 7–16 min. In one case, as an auroral arc propagated from the horizon toward the local zenith, the background E region wind field became significantly weaker but remained unaffected where the arc had not passed through. We demonstrate through modeling that these effects cannot be explained by height changes in the emission layer. The most likely explanation seems to be the greatly enhanced ion drag associated with the increased plasma density and localized ionospheric electric field associated with auroral arcs. In all cases, the F region neutral wind appeared less affected by the auroral arc, although its presence is clear in the data.