Hyper-encoding enables storing several qubits in a single photon using its different degrees of freedom like polarization and spatial ones. This approach enables feasible implementation of multi-qubit operations. One of the basic manipulations of two or more qubits is to swap their quantum state. Here we report on feasible and stable experimental implementation of a deterministic single photon two-qubit SWAP gate that interchanges path and polarization qubits. We discuss the principle of its operation and give detailed information about experimental demonstration employing two Mach-Zehnder interferometers with one common arm. The gate characterization is done by full quantum process tomography using photons produced by heralded single-photon source. The achieved quantum process fidelity reached more than 0.94 with an effective phase uncertainty of the whole setup, evaluated by means of Allan deviation, below 2.5 deg for 2.5 h without any active stabilization. Our design provides a contribution to the hyper-encoded linear quantum optics toolbox.