To investigate the effect of anions on the electrochemical properties of polyaniline (PANI) for supercapacitors, electrochemical performance tests of PANI with different dopant anions were carried out in the corresponding acid solutions by cyclic voltammetry (CV) and galvanostatic charge–discharge (GCD) methods. In particular, ionic fluxes and solvent molecules involved in redox processes can be analyzed by the electrochemical quartz crystal microbalance (EQCM) technique and discriminated by simultaneously recording cyclic voltammograms and mass changes during redox switching. The emeraldine base (EB) form of PANI prepared in a protonic acid with bigger anions can be easily doped by a protonic acid with smaller anions, and conversely, PANI-EB is hard to be doped. The anodic reversal potential of potentiodynamic cycling heavily influences the electrochemical stability of PANI. High anodic potentials result in PANI degradation. Its supercapacitive properties including specific capacitance, power density and cycling stability are strongly dependent upon the type of dopant anion. PANI with the dopant anions of oxalic acid has the highest specific capacitance and the best cycling stability among the used acids. The diffusion coefficient of anions plays a key role in determining power density. PANI films with organic dopant anions exhibit better cycling stability than their inorganic counterparts. It is believed that the hydrolysis of PANI facilitated by the additional water molecules accompanied by dopant anions into and out of the PANI matrix is a key factor responsible for the cycling instability.