Silica oligomerization is the key reaction in zeolite synthesis. NaOH is a common additive in the zeolite synthesis that decreases the reaction rate of smaller silica oligomers and also affects the final structure of the zeolite. Here we report a study of the role of sodium in the initial stages of silica oligomerization. We performed ab initio molecular dynamics simulations using explicit aqueous solution in order to obtain the free energy profile and study the behavior of sodium during the reaction. Our study confirms that sodium decreases the reaction rates of oligomerization for smaller silica chains. Analysis of the molecular dynamics trajectories shows that sodium does not increase the reaction barriers by direct coordination to the silica. However, sodium is often present in the second solvation shell of the reactive atoms. Correlation between sodium presence in the first or the second shell of the reactive oxygen and a decrease in hydrogen bonding for that oxygen was found for the first reaction step. Therefore, the presence of sodium could contribute to an increase in reaction barriers for silica oligomerization by some rearrangement of the hydrogen bond network of water solution around the reactants.