Crop production systems were used to show the presence and propagation of uncertainty in emergy analyses and the effect of source variance on the variance of the yield unit emergy value (UEV). Data on energy/masses and UEVs for each source and yield were collected from the emergy literature and considered as inputs for the Monte Carlo simulation. The inputs were assumed to follow normal, lognormal, or uniform probability distributions. Using these inputs and a tabular method, two models ran Monte Carlo simulations to generate yield UEVs. Supplemental excel files elucidate the Monte Carlo simulations' calculations. The nitrogen fertilizer UEV and net topsoil loss energy were the inputs with the largest impact on the variance of the yield's UEV. These two sources also make the largest emergy contributions to the yield and should be the focus of a manager intent on reducing total system uncertainty. The selection of a statistical distribution had an impact on the yield UEV and thus these analyses may need to remain system- or even source- specific.