In order to understand the counter anionic effects in a non-aqueous vanadium redox flow battery (VRFB), we synthesized four types of electrolyte salts (1-ethyltriethamine tertafluoroborate, [E-TEDA]+[BF4]−, 1-ethyltriethamine hexafluorophosphate, [E-TEDA]+[PF6]−, 1-butyltriethylamine tertafluoroborate, [B-TEDA]+[BF4]−, and 1-buthyltriethamine hexafluorophosphate [B-TEDA]+[PF6]−) by counter anion exchange reaction after the SN2 reaction. We confirmed the successful synthesis of the electrolyte salts [E-TEDA]+[Br]− and [B-TEDA]+[Br]− via 1H-NMR spectroscopy and GC-mass analysis before the counter anion exchange reaction. The electric potential of the vanadium acetylacetonate, V(acac)3, as an energy storage chemical was shown to be 2.2 V in the acetonitrile solvent with each of the [E-TEDA]+[BF4]−, [E-TEDA]+[PF6]−, [B-TEDA]+[BF4]−, and [B-TEDA]+[PF6]− electrolyte salts. In a non-aqueous VRFB with a commercial Neosepta AFN membrane, the maximum voltages reached 1.0 V and 1.5 V under a fixed current value of 0.1 mA in acetonitrile with the [E-TEDA]+[BF4]− and [E-TEDA]+[PF6]− electrolyte salts, respectively. The maximum voltage was 0.8 V and 1.1 V under a fixed current value of 0.1 mA in acetonitrile with the [B-TEDA]+[BF4]− and [B-TEDA]+[PF6]− electrolyte salts, respectively. From these results, we concluded that in the non-aqueous VRFB more of the [PF6]− counter anion than the [BF4]− counter anion was transported onto the commercial Neosepta AFN anion exchange membrane.