Reynolds-averaged Navier−Stokes (RANS) three-dimensional (3D) computational fluid dynamics (CFD) simulations of gaseous emissions from combustion engines are very demanding due to the complex geometry, the emissions formation mechanisms, and the transient processes inside the cylinders. The validation of emission simulation is challenging because of modeling simplifications, fundamental differences from reality (e.g., fuel surrogates), and difficulty in the comparison with measured emission values, which depend on the measuring position. In this study, detailed gaseous emission data were acquired for a spark ignition (SI) direct-injection (DI) single-cylinder engine (SCE) fueled with a toluene reference fuel (TRF) surrogate to allow precise comparison with simulations. Multiple devices in different sampling locations were used for the measurement of average emission concentration, as well as hydrocarbon (HC) cycle- and species-resolved values. A RANS 3D-CFD methodology to predict gaseous pollutants was developed and validated with this experimental database. For precise validation, the emission comparison was performed in the exact same locations as the pollutants were measured. Additionally, the same surrogate fuel used in the measurements was defined in the simulation. To focus on the emission prediction, the pressure and heat release traces were reproduced by calibrating a G-equation flame propagation model. The differences of simulation results with measurements were within 4% for CO2, while for O2 and NO, the deviations were within 26%. CO emissions were generally overestimated probably because of inaccuracies in mixture formation. For HC emissions, deviations up to 50% were observed possibly due to inexact estimation of the influence of the piston-ring crevice geometry. The reasonable prediction accuracy in the RANS context makes the method a useful framework for the analysis of emissions from SI engines, as well as for mechanism validation under engine relevant conditions.