The thermal stability of a series of dialkylimidazolium carboxylate ionic liquids has been investigated using a broad range of experimental and computational techniques. Ionic liquids incorporating fluoroalkyl carboxylate anions were found to have profoundly differing thermal stabilities and decomposition mechanisms compared with their non-fluorinated analogues. 1-Ethyl-3-methylimidazolium acetate was observed to largely decompose via an S(N)2 nucleophilic substitution reaction when under inert gas conditions, predominantly at the imidazolium methyl substituent. The Arrhenius equations for thermal decomposition of 1-ethyl-3-methylimidazolium acetate, and the C(2)-methylated analogue 1-ethyl-2,3-dimethylimidazolium acetate, were determined from isothermal Thermogravimetric Analysis experiments. The low thermal stability of 1-ethyl-3-methylimidazolium acetate has important implications for biomass experiments employing this ionic liquid. For these two ionic liquids, ion pair and transition state structures were optimised using Density Functional Theory. The activation barriers for the S(N)2 nucleophilic substitution mechanisms are in good agreement with the experimentally determined values.