The intensification of heat transfer using two-phase boiling flow in mini-channels is widely used to dissipate the high heat fluxes in miniaturized electronic devices. However, the process itself is not fully recognized and still requires experimental studies and developing computation methods appropriate for them. The main aim of this work was the mathematical modeling of time-dependent heat transfer process in FC-72 flow boiling in a mini-channel heat sink with five parallel mini-channels of 1 mm depth. Channels have an asymmetrically heated wall while its outer temperature was measured by infrared thermography. The opposite wall of the mini-channels was transparent, helping to record flow patterns due to a high-speed digital camera. The objective of the numerical calculations was to determine the heat transfer coefficient on the wall-fluid contact surface from the Robin boundary condition. The problem was solved using methods based on the Trefftz-type functions. Three mathematical methods were applied in calculations: the FEM with Trefftz type basis functions, the Classical Trefftz Method, and the Hybrid Picard-Trefftz Method. The results were compared with the values of the heat transfer coefficient obtained from theoretical correlations from the literature.