As hotspots become an increasingly important factor in the design of electronic devices, it has become essential to develop novel near-junction cooling methods. Steady-state thermoelectric cooling has previously been considered for the removal of localized hotspots on various substrates. In this paper, the transient behavior of a germanium thermoelectric self-cooler, in which the chip substrate is used as a leg of the thermoelectric circuit, is described. A 3-D thermoelectric numerical model was created in the commercial FEA package ANSYS and is used to explore the effects of various initial conditions, current pulse durations, current pulse magnitudes, pulse shapes, and die thicknesses. The results suggest that pulsed transient thermoelectric cooling has the potential to improve hotspot temperature reduction by approximately 30% relative to what is achievable in steady state. In addition, it was found that larger currents generally cause more rapid thermoelectric cooling, but also result in large overshoot temperatures and that the applied current profile has a strong effect on the transient behavior of the cooler.