This paper addresses the issue of thermoelectric cooling in a pulsed quasi-steady state (repetitive) condition. This situation occurs, for example, for an electronic integrated circuit performing demanding tasks in a discontinuous manner. Using heat reservoirs of selected capacity that are part of the thermoelectric system and appropriate shaping of the time profile of the supplied electrical current, cooling temperatures not achievable in the steady state for the system can be reached in a pulsed manner for a specified period. This process is subject to optimisation. The analysis was carried out for a two-stage system with an internal (interstage) heat reservoir of a given thermal capacity. The aim of the study was to find the relationship between the level of the supercooling temperature, its repeatability and the ability to maintain this temperature for a given time. To this end, two supply current waveforms were adopted and optimised both without and with contact thermal resistance in the system. The lowest subcooling temperature of about 7 K lower than the steady-state temperature was obtained for a very long period and a very short holding time. Decreasing the period or increasing the holding time results in a non-linear increase in temperature. Similar effects are obtained for the contact thermal resistance present in each layer. A full map of the period-thermal resistance–temperature relationship was determined, as well as the supercooling potential curves.