The calculation of time-dependent charge and energy currents in nanoscale systems is a challenging task. Nevertheless it is crucial for gaining a deep understanding of the relevant processes at the nanoscale. We extend the auxiliary-mode approach for time-dependent charge transport to allow for the calculation of energy currents for arbitrary time dependencies. We apply the approach to two illustrative examples, a single-level system and a benzene ring, demonstrating its usefulness for a wide range of problems beyond simple toy models, such as molecular devices.