AbstractThis paper discusses the state estimation and optimal control problem of a class of partially‐observable stochastic hybrid systems (POSHS). The POSHS has interacting continuous and discrete dynamics with uncertainties. The continuous dynamics are given by a Markov‐jump linear system and the discrete dynamics are defined by a Markov chain whose transition probabilities are dependent on the continuous state via guard conditions. The only information available to the controller are noisy measurements of the continuous state. To solve the optimal control problem, a separable control scheme is applied: the controller estimates the continuous and discrete states of the POSHS using noisy measurements and computes the optimal control input from the state estimates. Since computing both optimal state estimates and optimal control inputs are intractable, this paper proposes computationally efficient algorithms to solve this problem numerically. The proposed hybrid estimation algorithm is able to handle state‐dependent Markov transitions and compute Gaussian‐ mixture distributions as the state estimates. With the computed state estimates, a reinforcement learning algorithm defined on a function space is proposed. This approach is based on Monte Carlo sampling and integration on a function space containing all the probability distributions of the hybrid state estimates. Finally, the proposed algorithm is tested via numerical simulations.