While statistical estimation of uncertainty has not typically accompanied published emergy values, as with any other quantitative model, uncertainty is embedded in these values, and lack of uncertainty characterization makes their accuracy not only opaque, it also prevents the use of emergy values in statistical tests of hypotheses. This paper first attempts to describe sources of uncertainty in unit emergy values (UEVs) and presents a framework for estimating this uncertainty with analytical and stochastic models, with model choices dependent upon on how the UEV is calculated and what kind of uncertainties are quantified. The analytical model can incorporate a broader spectrum of uncertainty types than the stochastic model, including model and scenario uncertainty, which may be significant in emergy models, but is only appropriate for the most basic of emergy calculations. Although less comprehensive in its incorporation of uncertainty, the proposed stochastic method is suitable for all types of UEVs. The distributions of unit emergy values approximate the lognormal distribution with variations depending on the types of uncertainty quantified as well as the way the UEVs are calculated. While both methods of estimating uncertainty in UEVs have their limitations in their presented stage of development, this paper provides methods for incorporating uncertainty into emergy, and demonstrates how this can be depicted and propagated so that it can be used in future emergy analyses and permit emergy to be more readily incorporated into other methods of environmental assessment, such as LCA.