Temperature variation within a year can impact biological processes driving population abundances. The implications for the ecosystem services these populations provide, including food production from marine fisheries, are poorly understood. Whether and how temperature variability impacts fishery yields may depend on the number of harvested species and differences in their responses to varying temperatures. Drawing from previous theoretical and empirical studies, we predict that greater temperature variability within years will reduce yields, but harvesting a larger number of species, especially a more functionally diverse set, will decrease this impact. Using a global marine fisheries dataset, we find that within-year temperature variability reduces yields, but current levels of functional diversity (FD) of targeted species, measured using traits related to species' responses to temperature, largely offset this effect. Globally, high FD of catch could avoid annual losses in yield of 6.8% relative to projections if FD were degraded to the lowest level observed in the data. By contrast, species richness in the catch and in the ecosystem did not provide a similar mitigating effect. This work provides novel empirical evidence that short-term temperature variability can negatively impact the provisioning of ecosystem services, but that FD can buffer these negative impacts.