Pretreatment and hydrolysis of lignocellulosic biomass are affected by several uncertainties, which must be systematically considered for a robust process design. In this work, stochastic simulations for expected uncertainties in feedstock composition, kinetic parameter values, and operational parameter values for these two steps were performed. The results indicated that these uncertainties significantly impacted the concentration profiles, which could also affect the optimal batch time. Global sensitivity analysis was then used to identify the critical uncertain parameters. In the feedstock components, cellulose and xylan fractions for acid pretreatment and cellulose fraction for enzymatic hydrolysis were important. Temperature was the most sensitive operating parameter for both acid pretreatment and hydrolysis. The activation energies for different reactions were ranked in terms of their impact on process output. The selected parameters were used to develop stochastic process models using Ito process and mean reverting process for feed composition and kinetic parameter uncertainty.