Zinc ion ($Zn^{2+}$)-doped poly(3-methyl-thiophene)/multi-walled carbon nano tubes (MWCNT) composites (M-PMT-ZN) and poly(3-methyl-thiophene)/MWCNT composites (M-PMT) were synthesized by $in$ $situ$ chemical oxidative polymerization and investigated as electrode material for supercapacitors. The interactions of $Zn^{2+}$ ions with sulfur sites on the polymer chains were characterized by Fourier transform infrared spectroscopy. The morphology of the nanocomposites was characterized by scanning electron microscopy and high resolution transmission electron microscopy. The electrochemical properties were investigated using cyclic voltammetry, cyclic charging-discharging tests, and electrochemical impedance spectroscopy in a three-electrode system. Use of M-PMT-ZN resulted in a higher specific capacitance of 235 F/g. The specific capacitance retention after 500 cycles on M-PMT-ZN was also higher compared with that of the M-PMT composite. These results indicate that transition metal ion doping enhances the electrochemical properties of the conducting polymer.