This work presents experimental and numerical studies of heat transfer during cooling fluid flow in a group of five minichannels 1 mm deep. The main purpose was to determine the heat transfer coefficient on the contact surface between the fluid and the heated wall of the selected minichannel at subcooled boiling. The temperature distribution on the outer surface of the heated plate was measured by means of an infrared camera. Thermal and flow parameters were monitored by an appropriate data-acquisition system. The test section was placed horizontally with fluid flowing above the heated wall. The HFE-649, HFE-7100 and HFE-7200 working fluids were examined in the experiments. Simcenter STAR-CCM+ software was used for numerical analysis of heat transfer in the test section. Furthermore, a simplified two-dimensional (2D) model was proposed that designates subcooled boiling heat transfer during fluid flow in a central minichannel. The heat-transfer process in the heated plate and the working fluid was described using indicated partial differential equations with appropriate boundary conditions. The solution to the proposed system of equations led to the solving of two more inverse Cauchy-type problems. The classical Trefftz method (TM) and the homotopy perturbation method (HPM) combined with the TM allowed for obtaining temperature distributions in the heater and the fluid and consequently, the heat transfer coefficient at the heater–fluid interface from the Robin boundary condition. Comparison of the results from numerical simulation due to Simcenter STAR-CCM+ showed similar temperature distributions at the heated surface. The calculated heat transfer coefficients, by HPM and Simcenter STAR-CCM+, were validated using the 1D approach. Furthermore, the results from simulations in Simcenter STAR-CCM+ in the form of local temperatures of the heater were confronted with experimental data for comparison. Similar results were achieved.