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This work aims to explore the gas permeation performance of two newly-designed ionic liquids, [C2mim][CF3BF3] and [C2mim][CF3SO2C(CN)2], in supported ionic liquid membranes (SILM) configuration, as another effort to provide an overall insight on the gas permeation performance of functionalized-ionic liquids with the [C2mim]+ cation. [C2mim][CF3BF3] and [C2mim][CF3SO2C(CN)2] single gas separation performance towards CO2, N2, and CH4 at T = 293 K and T = 308 K were measured using the time-lag method. Assessing the CO2 permeation results, [C2mim][CF3BF3] showed an undermined value of 710 Barrer at 293.15 K and 1 bar of feed pressure when compared to [C2mim][BF4], whereas for the [C2mim][CF3SO2C(CN)2] IL an unexpected CO2 permeability of 1095 Barrer was attained at the same experimental conditions, overcoming the results for the remaining ILs used for comparison. The prepared membranes exhibited diverse permselectivities, varying from 16.9 to 22.2 for CO2/CH4 and 37.0 to 44.4 for CO2/N2 gas pairs. The thermophysical properties of the [C2mim][CF3BF3] and [C2mim][CF3SO2C(CN)2] ILs were also determined in the range of T = 293.15 K up to T = 353.15 K at atmospheric pressure and compared with those for other ILs with the same cation and anion’s with similar chemical moieties.