Optimization of the operating factors to achieve the maximum yield of biodiesel through transesterification reaction was performed by using face-centered central composite design (FCCD) approach of response surface methodology. A total of 29 independent batch experiments were considered in this model to carefully observe the effect of operating factors, such as the volume ratio of methanol/oil, catalyst (KOH) weight percent, reaction temperature, and reaction time. The FCCD model predicted that a maximum yield of 99.5% biodiesel would be achieved from flaxseed oil at a reaction temperature of 59 °C, 0.51% catalyst, the reaction time of 33 min, and a molar ratio of methanol to flaxseed oil of 5.9:1. Experimental verification of the predicted yield under the optimum conditions gave a maximum yield of 98 ± 2%, which is in very good agreement with the predicted value of the model. The physicochemical properties of the flaxseed oil-derived biodiesel were compared with those of standard biodiesel to identify and verify the quality of the produced biodiesel. All observed physicochemical parameters of the flaxseed oil-derived biodiesel were closely in agreement with those of standard biodiesel. Thus, demonstrating that the production of high-quality biodiesel from flaxseed oil is a viable option.