The thermal transesterification of cottonseed oil with methanol has been investigated. Refined as well as cotton seed oil containing 9.8 wt. % free fatty acids (FFAs) were used. The impact of the free fatty acids present in the oil on the transesterification reaction rates has been studied. Free fatty acids were esterified in parallel with triglycerides (TGs) methanolysis reactions but their presence was beneficial for transesterification reactions as they appeared to have a catalytic effect on the monoglycerides (MGs), diglycerides (DGs), and triglycerides conversion reactions. Experiments were performed in a batch reactor in the temperature range of 170-220 degrees C and using a 6:1 methanol to oil molar ratio. A kinetic model describing the thermal transesterification and esterification reaction as well as the catalytic transesterification reactions by the FFAs is presented. The proposed kinetics might also be used in transesterification processes using solid catalysts in the same temperature range to estimate the net catalytic effects unmasked from thermal conversion.