<p>In this paper, we consider a temporal and spatio-temporal within-host epidemic model and explore the model dynamics. Firstly, the sensitivity analysis of the temporal model parameters are performed using Latin Hypercube Sampling and PRCC method and the sensitive parameters are identified. The model is then extended to stochastic within-host model adding stochasticity to the sensitive parameters. Using Ito’s formula, the global existence and positivity of the solution is discussed. Stochastic boundedness, persistence, and the exponential stability of the infection-free equilibrium state are established. Secondly, the stochastic optimal control problem is formulated to investigate the effectiveness of the control measures. Finally, we extend the temporal model to the spatio-temporal model and discuss the global asymptotic stability of the infection-free state. Numerical simulations are conducted to validate the theoretical results. Environmental noise is found to play an important role in the control and persistence of the disease. By replicating and improving the results of deterministic model, we highlight the value added by the stochastic and spatio-temporal models in understanding the within-host disease dynamics.</p>