Reaching disability limits an individual's ability in performing daily tasks. Surface Functional Electrical Stimulation (FES) offers a non-invasive solution to restore lost ability. However, inducing desired movements using FES is still an open engineering problem. This problem is accentuated by the complexities of human arms' neuromechanics and the variations across individuals. Reinforcement Learning (RL) emerges as a promising approach to govern customised control rules for different settings. Yet, one remaining challenge of controlling FES systems for RL is unobservable muscle fatigue that progressively changes as an unknown function of the stimulation, thereby breaking the Markovian assumption of RL. In this work, we present a method to address the unobservable muscle fatigue issue, allowing our RL controller to achieve higher control performances. Our method is based on a Gaussian State-Space Model (GSSM) that utilizes recurrent neural networks to learn Markovian state-spaces from partial observations. The GSSM is used as a filter that converts the observations into the state-space representation for RL to preserve the Markovian assumption. Here, we start with presenting the modification of the original GSSM to address an overconfident issue. We then present the interaction between RL and the modified GSSM, followed by the setup for FES control learning. We test our RL-GSSM system on a planar reaching setting in simulation using a detailed neuromechanical model. The results show that the GSSM can help improve the RL's control performance to the comparable level of the ideal case that the fatigue is observable.