We present a detailed study of the H3+ auroral emissions at Jupiter, using data taken on 31 December 2012 with the long‐slit Echelle spectrometer CRIRES (ESO‐VLT). From this data set the rotational temperature of the H3+ ions in Jupiter's upper atmosphere was calculated using the ratio of the ν2 Q(1,0−) and ν2 Q(3,0−) fundamental emission lines. The entire northern auroral region was observed, providing a highly detailed view of ionospheric temperatures, which were mapped onto polar projections. The temperature range we derive in the northern auroral region is ~750–1000 K, which is consistent with past studies, although the temperature structure differs. We identify two broad regions which exhibit temperature changes over a short period of time (~80 minutes). We propose that the changes in temperature could be due to a local time change in particle precipitation energy, or they could be caused by dynamic temperature changes generated in the neutral thermosphere due to the magnetospheric response to a transient enhancement of solar wind dynamic pressure, as predicted by models. By comparing the H3+ temperature, column density, total emission, and line‐of‐sight velocity, we were unable to identify a single dominant mechanism responsible for the energetics in Jupiter's northern auroral region. The comparison reveals that there is complex interplay between heating by impact from particle precipitation and Joule heating, as well as cooling by the H3+ thermostat effect.