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 auxiliarymode 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.The transport and conversion of energy are of central importance for many biological systems and technological applications. Nanotechnology offers a route to make use of the efficiency and robustness found in nature for energy harvesting and energy transduction in nano-scale devices. To take full advantage of the possibilities provided by molecular junctions [1,2] or quantum dot arrays [3,4], a deep understanding of the involved dynamical processes is necessary. Here, the theoretical description of time-dependent transport of charge and energy can contribute valuable insights and help to find new applications [5,6].