Transfer of phonons through a silicon–diamond thin film pair with a nano-size gap at the interface is examined. The thin film pair is thermally disturbed by introducing 301 K at the silicon film left edge while keeping the other edges of the thin films at a low temperature (300 K). The radiative phonon transport equation is solved numerically to quantify the phonon intensity distribution in the combined films. The frequency dependent formulation of phonon transport is incorporated in the transient analysis. The thermal boundary resistance is adopted at the interface in the formulations. The near-field radiative heat transfer is also adopted at the gap interface, as the vacuum gap size falls within the Casimir limit. The predictions of thermal conductivity are validated through the thermocouple data. It is observed that predictions of thermal conductivity are in agreement with the experimental data. The ballistic phonons play a major role in energy transfer through the gap; their contribution is more significant than that of the near-field radiative heat transfer. Enlarging the size of the gap reduces the influence of the ballistic phonons on the energy transfer in the films. Increasing the silicon film thickness alters the energy transfer through the gap; in this case, the equivalent equilibrium temperature difference is increased at the interface.