A base-catalysed methyltrimethoxysilane (MTMS) colloidal gel formation was implemented as a cellular automaton (CA) system, specifically diffusion and/or reaction-limited aggregation. The initial characteristic model parameters were determined based on experimental synthesis of MTMS-based, ambient-pressure-dried aerogels. The applicability of the numerical approach to the prediction of gels' condensation kinetics and their structure was evaluated. The developed model reflects the kinetics properly within the investigated chemical composition range (in strongly reaction-limited aggregation conditions) and, to a slightly lesser extent, the structural properties of aggregates. Ultimately, a relatively simple numerical model reflecting silica-based gel formation was obtained and verified experimentally. The CA simulations have proved valid for understanding the relation between the initial chemical composition and kinetics constants of MTMS-based synthesis and their impact on secondary particle aggregation process kinetics.