Recently, several groups have reported spin-dependent thermoelectric effects in magnetic tunnel junctions. In this paper, we present a setup for time-resolved measurements of thermovoltages and thermocurrents of a single micro-to nanometer-scaled tunnel junction. An electrically modulated diode laser is used to create a temperature gradient across the tunnel junction layer stack. This laser modulation technique enables the recording of time-dependent thermovoltage signals with a temporal resolution only limited by the preamplifier for the thermovoltage. So far, time-dependent thermovoltage could not be interpreted. Now, with the setup presented in this paper, it is possible to distinguish different Seebeck voltage contributions to the overall measured voltage signal in the µs time regime. A model circuit is developed that explains those voltage contributions on different sample types. Further, it will be shown that a voltage signal arising from the magnetic tunnel junction can only be observed when the laser spot is directly centered on top of the magnetic tunnel junction, which allows a lateral separation of the effects.