Temperature profiles derived from Cassini Ion Neutral Mass Spectrometer data in Paper I show that the thermal structure of Titan’s upper atmosphere is extremely variable. The median temperature of each vertical profile, which is approximately equal to the temperature derived by fitting the barometric equation to the N2 density profile, varied between 112 and 175K. Here we attempt to understand the cause of the 60K variation in temperature, as well as large local perturbations in temperature, by estimating the strength of potentially important energy sources and sinks in Titan’s thermosphere including ion and electron precipitation from Saturn’s magnetosphere, Joule heating, and wave dissipation. The apparent correlation between the temperature of Titan’s thermosphere and Titan’s plasma environment suggest that particle precipitation from Saturn’s magnetosphere may be the most significant heat source, but we find that the energy deposited by magnetospheric sources is less than solar EUV and results from a thermal structure model indicate that magnetospheric particle precipitation only increases the temperature of Titan’s thermosphere by ∼7K; therefore, heating due to magnetospheric particle precipitation is too small to explain the largest temperature variations observed. We also estimate the energy deposited by waves in Titan’s thermosphere and show that wave dissipation may be a significant source of heating or cooling in Titan’s upper atmosphere.