Enhanced mid-infrared emission from CH4 and other stratospheric hydrocarbons has been observed coincident with Jupiter’s ultraviolet auroral emission1–3. This suggests that auroral processes and the neutral stratosphere of Jupiter are coupled; however, the exact nature of this coupling is unknown. Here we present a time series of Subaru-COMICS images of Jupiter measured at a wavelength of 7.80 μm on 11–14 January, 4–5 February and 17–20 May 2017. These data show that both the morphology and magnitude of the auroral CH4 emission vary on daily timescales in relation to external solar-wind conditions. The southern auroral CH4 emission increased in brightness temperature by about 3.8 K between 15:50 ut, 11 January and 12:57 ut, 12 January, during a predicted solar-wind compression. During the same compression, the northern auroral emission exhibited a duskside brightening, which mimics the morphology observed in the ultraviolet auroral emission during periods of enhanced solar-wind pressure4,5. These results suggest that changes in external solar-wind conditions perturb the Jovian magnetosphere in such a way that energetic particles are accelerated into the planet’s atmosphere, deposit their energy as deep as the neutral stratosphere, and modify the thermal structure, the abundance of CH4 or the population of energy states of CH4. We also find that the northern and southern auroral CH4 emission evolved independently between the January, February and May images, as has been observed at X-ray wavelengths over shorter timescales6 and at mid-infrared wavelengths over longer timescales7.