The gas flow modulation technique is a recently proposed approach for measuring the axial gas dispersion coefficient in bubble columns. This study presents a quantitative analysis of the experimental uncertainty associated with gamma-ray densitometry and ensemble-averaging of the data. The considered uncertainty sources are the statistics of the photon counting process, a mismatch between the modelled and the real radiation propagation due to the spatial extent of the detector, and a potential mismatch between modulation and sampling frequencies. The analysis is based on a numerical gamma-ray propagation model and a Monte Carlo approach to account for statistical uncertainty. The proposed algorithm supports the selection of an optimal total scanning time based on detector size, modulation parameters, involved fluids and column and source parameters. The analysis reveals that a mismatch between the modulation and sampling frequencies is most critical while the impact of the other considered uncertainty sources is rather marginal.