Our study demonstrates successful error mitigation of indistinguishably-related noise in a quantum photonic processor through the application of the zero-noise extrapolation (ZNE) technique. By measuring observable values at different error levels, we were able to extrapolate toward a noise-free regime. We examined the impact of partial distinguishability of photons in a two-qubit processor implementing the variational quantum eigensolver for a Schwinger Hamiltonian. Our findings highlight the effectiveness of the extrapolation technique in mitigating indistinguishably-related noise and improving the accuracy of the Hamiltonian eigenvalue estimation.