The aim of this study is to determine the heat transfer coefficient between the heated surface and the boiling fluid flowing in a minichannel on the basis of experimental data. The calculation model is based on Beck’s method coupled with the FEM and Trefftz functions. The Trefftz functions used in the Hermite interpolation are employed to construct the shape functions in the FEM. The unknown local values of the heat transfer coefficient at the foil- -fluid contact surface are calculated from Newton’s law. The temperature of the heated foil and the heat flux on the foil surface are determined by solving a two-dimensional inverse heat conduction problem. The study is focused on the identification of the heat transfer coefficients in the subcooled boiling region and the saturated nucleate boiling region. The results are compared with the data obtained through the one-dimensional method. The investigations also reveal how the smoothing of measurement data affects calculation results.