Mathematical analysis and simulation of a discontinuous rectification column was performed using an operational strategy during the start-up before reaching a pseudo-stable state in discontinuous operation. The mathematical model was formulated focusing on the equilibrium state (ES) and implementing MESH equations (M: Mass balance, E: Equilibrium thermodynamics, S: Stoichiometry relations, H: Enthalpy or heat balance) to provide solutions using the Thomas method and the Wang-Henke algorithms internally coupled to the Fourth Order Runge-Kutta method. The results were validated with experimental data from a distillation column at a pilot scale using an ethanol-water system with an equilibrium behavior described by the UNIQUAC Functional-group Activity Coefficients (UNIFAC) and Predictive Soave-Redlich-Kwong (PSRK) thermodynamic models with a global error of 1.84%. The molar ethanol concentrations presented deviations from the mathematical model predictions from 1.51% to 0.02%, with a global mean error of 0.48%. A mean error of 0.055% was obtained for the temperature profile of the column, thus demonstrating the effectiveness of the solution and its convergence capacity. The solution based on the Thomas method and the Wang-Henke algorithms coupled to the Runge-Kutta method made it possible to describe the behavior and variables of all stages of the distillation column. Operation at total reflux from start-up avoids wasting product and allows for the stabilization of the state variables, such as temperature and molar composition.