The paper deals with mathematical modeling of heat transfer phenomena occurring in a system containing thermoelectric elements. The main focus was on creating a useful computational tool for designing, validating, testing, controlling, and regulating the energy harvesting system with a thermoelectric cell. The model widely described in the literature, assuming a constant temperature level on both sides of the cell, has been modified to take into account the thermal resistance of heat exchangers that are inseparable parts of nearly every device of this kind. The results and conclusions from the solutions of equations forming a formalized record of the proposed method, the assumed approach to modeling, used physical phenomena and sensitivity analysis of the impact of the tested parameters on the system operation was presented. The calculations were made for the data of a selected thermoelectric generating cell available on the market.