Transesterification of waste cotton cooking oil (WCCO) is reported here. The GC-MS analysis of WCCO oil was studied and the major fatty acids were found to be Palmitic acid (28.26%) and Linoleic acid (43.14%). The molecular weight of the oil was 872.049 g/mol (GC-MS). The results showed maximum biodiesel yield of 96% when the reaction temperature, time, methanol/oil ratio and catalyst loading were fixed at 65°C, 45 min, 6:1 and 2% (wt.%) respectively. Partial purification of the biodiesel was performed for better engine performance and improved emission characteristics. The flash point and fire point of WCCO biodiesel were found to be 158°C and 165°C respectively. The brake thermal efficiency of WCCO10 biodiesel was 26.64% for maximum load and the specific fuel consumption for diesel was 0.3479 kg/kWh at maximum load. The use of biodiesel blends showed a reduction of carbon monoxide and hydrocarbon emissions and a marginal increase in nitrogen oxide emissions. © 2016 Informa UK Limited, trading as Taylor & Francis Group.