Transesterification of rapeseed oil with methanol was investigated over a heterogeneous catalysis system using sodium modified fluorapatite (Na/FAP) as a highly efficient, solid, bi-functional catalyst. Several parameters such as the impregnation ratio, calcination temperatures and catalyst loading were investigated and optimized for maximum biodiesel yield. The basic properties of the catalyst were estimated by phenol adsorption. The suitable reaction conditions for maximum biodiesel yield of 98% are the methanol to oil molar ratio of 10:1, temperature of 120 °C and reaction time of 8 h, with a 6 wt% of catalyst to oil weight ratio. The recycling studies have shown that the catalyst can be readily recovered and reused at least five consecutive cycles with significant loss of the activity. Several important physicochemical properties of the obtained biodiesel were evaluated and the results were compared with the standards for biodiesel specifications as described by EN14214. Results from waste cooking oil transesterification indicated that a FAME yield of 97% could be obtained by two-step transesterification process, thus giving rise to a potentially applicable possibility in biodiesel production from used cooking oil.