An analysis of wavelength‐dependent absorption in 229 FUV spectra (1150–1950 Å) of the Jovian north polar emissions obtained with the International Ultraviolet Explorer over the period 1978–1989 shows that the hydrocarbon optical depth in front of the auroral emission has a consistent dependence on the Jovian magnetic longitude. This variation is interpreted in two distinct ways: (1) the Jovian upper atmosphere is longitudinally homogeneous, and the variation in optical depth is due to a variation in penetration, and thus energy, of the primary particles; or (2) the energy of the primaries is longitudinally homogeneous, and it is aeronomic properties which change, most likely as a result of auroral heating. For case 1, the estimates of energy per particle for each of four particles which have been proposed as auroral primaries vary by a factor of ∼1.5–3.2 as a function of magnetic longitude, depending on the identity of the particles considered; the atmospheric model‐dependent energies are of the order of 14 keV for electrons, 0.4 MeV for protons, 0.4 MeV/nucleon for oxygen, and 0.3 MeV/nucleon for sulfur ions in a simple model polar atmosphere which we propose. Energy estimates for oxygen and sulfur ions fall well within limits established by Voyager measurements of the population of energetic O and S ions in the magnetosphere. For case 2, changes in atmospheric properties are modeled as a variation in the eddy diffusion coefficient K in the polar model, which covers the range from ∼3×106 to 2×107 cm² s−1, consistent with expected effects of localized auroral heating. Both interpretations imply a remarkable degree of stability in the coupling of the magnetosphere and atmosphere during the period of the observations, which covers a complete solar cycle and includes the Voyager encounters with Jupiter.