The Fourier and the hyperbolic heat conduction equations were solved numerically to simulate a frequency-domain thermoreflectance (FDTR) experiment. Numerical solutions enable isolation of pump and probe laser spot size effects and use of realistic boundary conditions. The equations were solved in time domain and the phase lag between the temperature of the transducer (averaged over the probe laser spot) and the modulated pump laser signal was computed for a modulation frequency range of 200 kHz–200 MHz. Numerical calculations showed that extracted values of the thermal conductivity are sensitive to both the pump and probe laser spot sizes, while analytical solutions (based on Hankel transform) cannot isolate the two effects. However, for the same effective (combined) spot size, the two solutions are found to be in excellent agreement. If the substrate (computational domain) is sufficiently large, the far-field boundary conditions were found to have no effect on the computed phase lag. The interface conductance between the transducer and the substrate was found to have some effect on the extracted thermal conductivity. The hyperbolic heat conduction equation yielded almost the same results as the Fourier heat conduction equation for the particular case studied. The numerically extracted thermal conductivity value (best fit) for the silicon substrate considered in this study was found to be about 82–108 W/m/K, depending on the pump and probe laser spot sizes used.