Understanding population extinctions is a chief goal of ecological theory. While stochastic theories of population growth are commonly used to forecast extinction, models used for prediction have not been adequately tested with experimental data. In a previously published experiment, variation in available food was experimentally manipulated in 281 laboratory populations of Daphnia magna to test hypothesized effects of environmental variation on population persistence. Here, half of those data were used to select and fit a stochastic model of population growth to predict extinctions of populations in the other half. When density-dependent demographic stochasticity was detected and incorporated in simple stochastic models, rates of population extinction were accurately predicted or only slightly biased. However, when density-dependent demographic stochasticity was not accounted for, as is usual when forecasting extinction of threatened and endangered species, predicted extinction rates were severely biased. Thus, an experimental demonstration shows that reliable estimates of extinction risk may be obtained for populations in variable environments if high-quality data are available for model selection and if density-dependent demographic stochasticity is accounted for. These results suggest that further consideration of density-dependent demographic stochasticity is required if predicted extinction rates are to be relied upon for conservation planning.