Heat pulse (HP) measurements are used as an alternative method for a variety of thermal and hydraulic properties critical for many scientific disciplines and engineering applications. This study investigated factors affecting heat pulse probe (HPP) measurements using COMSOL numerical simulations. We sought to understand the influence of rod support material (e.g., circuit board) and rod length on the measured temperature rise by comparing the parametric model-fitted thermal properties of ice and water with the known reference values. Temperature dynamics near the rod support were significantly impacted by the physical and thermal properties of the rod support material, while temperature changes further away from it were mostly affected by the properties of the surrounding media. In addition, comparing results for soil volumetric water contents of 0.00, 0.20, and 0.40 m3 m−3, thermal variations near the rod support material were greater at lower water contents. Results indicate the rod length should be 60 mm or longer, and the optimal thermistor location is at the midpoint of the rod, where more accurate temperature rise curves were obtained for both measurements and simulations.