Drought stress severely affects global plant growth and production. The enhancement of plant water-use efficiency (WUE) and drought tolerance by the manipulation of the stomata is an effective strategy to deal with water shortage. However, increasing the WUE and drought tolerance by manipulation on the stomata has rarely been tested inBrassica napus. Here, we isolatedBna.EPF2, an epidermal patterning factor (EPF) inBrassica napus(ecotype Westar), and identified its role in drought performance.Bna.EPF2overexpression lines had a reduction average of 19.02% in abaxial stomatal density and smaller stomatal pore size, leading to approximately 25% lower transpiration, which finally resulted in greater instantaneous WUE and enhanced drought tolerance. Interestingly, the reduction in stomatal density did not affect the CO2assimilation or yield-related agronomic traits inBna.EPF2overexpression plants. Together with the complementation ofBna.EPF2significantly decreasing the stomatal density of Arabidopsisepf2, andBna.EPF2being expressed in mature guard cells, these results suggest thatBna.EPF2not only functions in stomatal density development, but also in stomatal dimension in Brassicas. Taken together, our results suggest thatBna.EPF2improves WUE and drought tolerance by the regulation of stomatal density and stomatal size in Brassica without growth and yield penalty, and provide insight into the manipulation of this gene in the breeding of drought tolerant plants with increased production under water deficit conditions.