The legacy electromagnetic (EM) pump analysis tool MATRIX has been improved by the addition of a thermal analysis module. Although the module is patterned after the general-purpose Advanced General Electric Network Analyzer (AGENA) code, it is developed from a more fundamental approach to provide a better understanding and control of the thermal analysis of the EM pump. The MATRIX results are verified against the AGENA results and the test data from the 160 m3/min large EM pump tests, which provided a good estimate of the thermal conductance between the lamination and the inner duct wall. Full and good contact between the lamination and the inner duct wall is necessary to keep the copper conductor temperatures low. Parametric studies, as expected, confirmed the correct trend of increasing copper conductor temperatures with increasing frequency. The MATRIX results show that a new proposed insulation material for the future EM pumps is beneficial since it could reduce the copper block temperature by ~20°C. Such analysis can help develop a better EM pump with a more compact design and better insulation material.