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Microwave-assisted transesterification due to drastic reduction in reaction time when compared with conventional method gain the research attention. Pesent study explores the kinetic and thermodynamic study of microwave-assisted transesterification of non-edible papaya oil. The experiments were performed using pre-optimized process parameters having 9:1 molar ratio of methanol to oil, 1 wt. % NaOH catalyst. The experiments carried out in commercial microwave reactor with infrared temperature controller. Kinetic study of microwave-assisted palm oil methyl ester (POME) conversion was carried out by varying temperature from 50 to 65 ºC with an increment of 5 ºC. Kinetic study revealed that microwave-assisted homogeneous alkali-catalyzed transesterification follows first order having lower activation energy 27.86 KJ mol-1. Also, higher frequency factor 14764 min-1 and rate constant 0.6703 min-1 at 60 ºC revealed the non-thermal and thermal effect of the microwave. Other thermodynamic properties such as ΔG, ΔH and ΔS were found out to be 94.48 KJ/mol, 24.87 KJ/mol and -0.209 KJ/mol K, respectively, which show that reaction is non-spontaneous, endothermic and endergonic in nature.