Real-time scheduling problems increase the practical implementation of the manufacturing system. In this study, using a single objective performance measure i.e., Number of Tardy Jobs (NTJ), the influence of 5 input constraints, i.e., reliability level (R_L), percentage of machine failure (%McF), mean time to repair for random machine breakdown (MTR_RMcB), due date tightness factor (Ғ), and routing flexibility level (R_FL) were evaluated for considered stochastic Flexible Job Shop Scheduling Problem (FJSSP). The study integrated reliability-centered preventive maintenance (PMRC) and random machine breakdown (RMcB) environment with sequence-dependent setup time in the considered problem. A statistical response surface methodology was used to assesses NTJ. A second-order regression model was obtained to compute correlation between input constraints and NOTJ at 95% confidence level. The results demonstrate that main effects of R_L, %McF, Ғ, and R_FL; the interaction effects of R_L and Ғ, %McF and R_FL, MTR_RMcB and R_FL, and Ғ and R_FL; and quadratic effects of Ғ and R_FL, have significant impact on NTJ performance measure. Ғ has emerged as the major factor affecting NTJ. The confirmatory data demonstrate that error is less than 5%, confirming model can be used for future computations. Further, the novelties of the work are shown by the fact that it takes into account the uncertainties in the scheduling issue, as well as the dynamic tasks arrival environment. The aforementioned findings will assist production managers in planning and scheduling flexible job shops in order to satisfy customer demand on time.