This study was performed to investigate the applicability of the basic heterogeneous fluorapatite catalyst prepared from waste animal bones in the transesterification of waste cooking oil with methanol for production of biodiesel. Response surface methodology based on D-optimal design of experiments was employed to study the significance and interactive effect of methanol to oil (M:O) molar ratio, catalyst concentration, reaction time, and mixing rate on biodiesel yield using the prepared fluorapatite and Novozym 435. Quadratic model equations were obtained describing the interrelationships between dependent and independent variables to maximize the response variable (biodiesel yield) and the validity of the predicted models were confirmed. The optimum combination for transesterification were determined to be 7.35:1 and 6:1 M: O, 4.35 and 8.8 catalyst wt%, 91 and 96 min, and 331 and 394 rpm at 60 degrees C, for prepared fluorapatite and Novozym 435, respectively, with maximum biodiesel yield of approximate to 96 and 62%, respectively. Fuel properties of the produced biodiesel and its blends with petro-diesel were measured and compared with those of Egyptian petro-diesel and international biodiesel standards. Acceptable agreement was observed, encouraging application of fluorapatite prepared from waste animal bones for production of biodiesel as an alternative or complementary to petro-diesel.