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We present a new state tracking algorithm based on a stochastic state reassignment that reflects the quantum mechanical interpretation of the state time-overlaps. We assess the new method with a range of model Hamiltonians and demonstrate that it yields the results generally consistent with the deterministic min-cost algorithm. However, the stochastic state tracking algorithm reduces magnitudes of the state population fluctuations as the quantum system evolves toward its equilibrium. The new algorithm facilitates the thermalization of quantum state populations and suppresses the population revivals and oscillations near the equilibrium in many-state systems. The new stochastic algorithm has a favorable computational scaling, is easy to implement due to its conceptual transparency, and treats various types of state identity changes (trivial or avoided crossings and any intermediate cases) on equal footing.