Although manganese oxide (MnO2) can be incorporated with vertically aligned carbon nanotubes (VACNTs) to improve supercapacitor performance potentially, one of the hurdles that hampers this embodiment is a difficulty of coating MnO2 on VACNTs homogeneously. As a way of overcoming this hurdle, we present here a facile method of pulsed current electrodeposition that turns out to exceed conventional methods in coating quality. Such improvement leads to a clear enhancement in gravimetric specific capacitance, reaching a state-of-the-art value of 243.3 F/g at a high scanning rate of 100 mV/s. In the course of this characterization, diffusion hindrance through a MnO2 layer clogging over VACNTs is found out to limit the device performance at high mass loading. An empirical relationship is proposed to explain such phenomenon and demonstrates good application in various conditions. The optimized VACNTs/MnO2 electrode also reveals outstanding high-rate performances.