A detailed methodology for conducting experiments in batch reactors is proposed. Hydrodesulfurization of petroleum distillates in a laboratory-scale batch reactor is taken as an example. Reaction parameter calculations and a data reconciliation method are described in detail. Reaction parameters depend on the aim of the experimentation; in this work, absolute and percentage errors of the global and elemental (C, H, S, and N) mass balances, hydrodesulfurization percentage, product yields, and hydrogen consumption were selected. Three distinct data sets of results were obtained for the mass balances, each one involving a different gas mass determination procedure, i.e., direct weighing, from the measured gas volume with a gasometer, and from the pressure inside the batch reactor at room temperature. The lowest errors of the global and elemental balances were obtained from the gas volume measurement and the highest from the reactor pressure approach; however, all of the calculated mass balance percentage errors are lower than 1%, and the reaction parameters are in good agreement between them, which indicates that the experimental procedure was adequately performed. The proposed data reconciliation method can also be applied to the correction of mass balance results of other experiments and reactions, but careful assessment of the reliability of the mass measurements of the feeds, products, and catalysts (if used) should be previously made. After the application of the data reconciliation method to the mass balance results calculated from the reactor pressure, the masses of the gaseous feed and product were closer to the respective calculated masses from the gas volume, which confirms their accuracy.