Abstract <p>The problem of reconstructing an unknown time-dependent Hamiltonian of a two-level quantum system from data on the system’s dynamics is considered. A method based on a neural network within the Neural ODE framework is proposed, in which the continuous evolution of the quantum state is modeled by integrating the Schrödinger equation with a parametric Hamiltonian model implemented by the network. As input data, measured time series of the expectation values of Pauli operators for a qubit are used. The network is trained by minimizing the difference between the experimentally observed and modeled trajectories of quantum observables. Using the example of simulating spin dynamics in a time-varying magnetic field, it is shown that the proposed approach enables high-accuracy reconstruction of the time-dependent Hamiltonian parameters without interrupting the quantum evolution. The results demonstrate that the Neural ODE model provides continuous tracking of the time parameter and reliable reconstruction of the system’s dynamics under conditions of limited data and noise.</p>