A conceptually new approach has been developed for the fabrication of MnO2-multiwalled carbon nanotube (MWCNT) composites for electrodes of electrochemical supercapacitors (ES). Benzyldimethylhexadecylammonium chloride (BAC) surfactant and caffeic acid (CA) selectively adsorbed on MWCNT and MnO2, respectively, and allowed the formation of stable aqueous suspensions of positively charged MWCNT and negatively charged MnO2. The comparison of the electrophoretic deposition yield data for BAC, CA and other molecules provided an insight into the influence of the molecular structure on adsorption of the molecules and dispersion of MWCNT and MnO2. Advanced composite materials with good mixing of the individual components were obtained by heterocoagulation, based on an ion-pairing assembly of BAC and CA. The composite electrodes, prepared by the new method showed superior electrochemical performance. It was found that high capacitance and good capacitance retention at high charge–discharge rates can be achieved at high active mass loadings. A practical outcome of this study was the fabrication of an asymmetric SC device, containing a positive MnO2–MWCNT electrode and negative activated carbon–carbon black composite electrode with a voltage window of 1.8 V in an aqueous electrolyte. The asymmetric device showed high capacitance, high power-energy characteristics, good capacitance retention at high charge–discharge rates and cyclic stability.