The rapid growth of biodiesel industry has led to a large surplus of its major unintentional byproduct particularly glycerol. Thus, finding a new application is necessary to convert glycerol to value added products. In this study, glycerol has been subjected to a transesterification reaction to synthesis glycerol carbonate (GC) over several selected ammonium and imidazolium-based ionic liquids (ILs) as catalysts. It is believed that the variation of catalytic performance between ILs was due to the anion strength of ILs. The glycerol conversion, yield and selectivity of GC were followed the anion order of [Ac]>[Dca]>[Fmt]>[DMP]>[NO3]>[Cl]>[BF4]. Effects of reaction temperature, time, diethyl carbonate (DEC)/glycerol molar ratio and catalyst loading on glycerol conversion and GC yield have been analysed. The IL, 1-ethyl-3-methylimidazolium acetate (emim[Ac]) shows best performance under solvent-free with conversion of glycerol and GC yield reached highest at 93.50% and 88.70%, respectively under reaction temperature of 120°C reaction time of 2h, DEC/glycerol molar ratio of 2 and catalyst loading of 0.5mol%. Also, this emim[Ac] can be reused as catalyst at least three times without any significant reduction in conversion, yield and selectivity. Reaction mechanism of the transesterification reaction catalysed by emim[Ac] has been proposed in this study.