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Turbulent mixing induces variability in concentration that is important in many applications, such as reactive plumes, risk assessments or odour impact analyses (when the effects can have time scales on the order of a second). In urban canopies, the variability may be modified by the presence of buildings. Our purpose is to study concentration fluctuation variance in built-up areas using an Eulerian approach. We performed numerical simulations with the computational fluid dynamics model Mercure_Saturne, which is a three-dimensional model adapted to atmospheric flow and pollutant dispersion. We use a k - epsilon turbulence closure and predict the concentration variance with a transport equation model. The model performance is evaluated with the near-full scale experiment MUST (Mock Urban Setting Test), a field experiment conducted in Utah’s West Desert Test Center. The modelled root-mean-square of the concentration fluctuations is compared to measurements for 20 of the MUST trials. The model shows good agreement with the measurements, with the fraction of predictions within a factor of two of observations of 60.1%, with better results for horizontal lines of detectors than for the detectors on vertical masts (with fractions of predictions within a factor of two of observations of respectively 66.4% and 52.6%). The influence of different parameters on the fluctuation variance is also studied and we show the importance of taking into account the stability of the stratification when modelling the turbulent kinetic energy.