Harvest control rules are widely used by management agencies for decision-making and for promoting public awareness of the status of marine and freshwater fisheries. Many current control rules combine fishing mortality and biomass-based biological reference points. Control rules were introduced as a precaution against the influence of uncertainty and to decrease the risk of overfishing, but are compromised if the uncertainties of the biological reference points are not explicitly considered. Uncertainty has been widely acknowledged but has not been incorporated into control rule design and application. In this paper, we used a Bayesian statistical catch-at-age model to estimate uncertainties in the indicators of fishing mortality, population size, and biological reference points. We apply this model to the Lake Erie walleye (Sander vitreus) fishery, and by fully considering the uncertainty of the indicators, the risk of overfishing and the risk of the population being overfished can be explicitly estimated in the control rules. We suggest short and long-term approaches to incorporate uncertainty in the design of control rules. We also suggest that control rules for specific fisheries should be designed with explicit consideration of the uncertainty of the biological reference points, based on a risk level that the management agency and stakeholders agree upon.