BMIM PF6 (1-butyl-3-methylimidazolium hexafluorophosphate) and BMIM Tf2N (1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide) are two conventional room-temperature ionic liquids widely employed and investigated as reaction media. Despite the presence of the same imidazolium ring in their structure they are different in many chemical and physical properties due to the nature of the anions. The thermal cis-trans isomerization of an electronically activated azobenzene have been used as reaction model to compare the behavior of PF6− and Tf2N−. Rotation is the mechanism by which the investigated azobenzene is converted into the trans isomer spontaneously in the dark both in BMIM PF6 and in BMIM Tf2N. The kinetic rate constants of the process have been determined at different temperatures and the activation energies of the reaction have been calculated according to the Arrhenius and Eyring equations. The results presented herein highlight different solute-solvent interactions involving the PF6− and Tf2N− anions during the cis-trans isomerization.