Past observations and modeling of Jupiter's thermosphere have, due to their limited resolution, suggested that heat generated by the aurora near the poles results in a smooth thermal gradient away from these aurorae, indicating a quiescent and diffuse flow of energy within the subauroral thermosphere. Here we discuss Very Large Telescope-Cryogenic High-Resolution IR Echelle Spectrometer observations that reveal a small-scale localized cooling of ~200 K within the nonauroral thermosphere. Using Infrared Telescope Facility NSFCam images, this feature is revealed to be quasi-stable over at least a 15 year period, fixed in magnetic latitude and longitude. The size and shape of this “Great Cold Spot” vary significantly with time, strongly suggesting that it is produced by an aurorally generated weather system: the first direct evidence of a long-term thermospheric vortex in the solar system. We discuss the implications of this spot, comparing it with short-term temperature and density variations at Earth.