Quantum system inversion concerns learning the characteristics of the underlying Hamiltonian by measuring suitable observables from the responses of the system's interaction with members of a set of applied fields. Various aspects of inversion have been confirmed in theoretical, numerical and experimental works. Nevertheless, the presence of noise arising from the applied fields may contaminate the quality of the results. In this circumstance, the observables satisfy probability distributions, but often the noise statistics are unknown. Based on a proposed theoretical framework, we present a procedure to recover both the unknown parts of the Hamiltonian and the unknown noise distribution. The procedure is implemented numerically and seen to perform well for illustrative Gaussian, exponential and bi-modal noise distributions.