The quest for the development of promising electrode materials for energy storage persists. Interest in transition metal chalcogenides is growing rapidly for the development of better electrochemical capacitors. In recent years, transition metal chalcogenides have emerged as high performance electrode materials when compared to transition metal oxides due to their multiple oxidation states, promoting a rapid redox reaction, and their high electrical conductivity. In this study, MnSe acts as a highly conductive material as well as influencing rapid ion transfer and ion storage. MnSe supports a solid base structure, reducing the diffusive capacitive behaviour and increasing the surface charge transfer of NiCo2O4. Manganese selenide (MnSe) and heterostructure manganese selenide (MnSe)/nickel cobalt oxide (NiCo2O4) were synthesized using an electrodeposition technique and examined for their performance as an electrode material for supercapacitors. Physical characterization, such as X-ray diffraction, field emission scanning electron microscopy, X-ray photoelectron spectroscopy and transmission electron microscopy, revealed the formation and structure of the MnSe and MnSe(20)/NiCo2O4 working electrode. For the first time, electrodeposited MnSe and MnSe(20)/NiCo2O4 electrochemical behaviour was studied and analysed. The electrodeposited MnSe and MnSe(20)/NiCo2O4 single electrode showed a specific capacitance of 184.92 F g−1 and 450.75 F g−1, respectively, at a current density of 0.1 A g−1. Besides, the MnSe(20)/NiCo2O4 asymmetric cell revealed a specific capacitance of 45.78 F g−1 at a current density of 0.1 A g−1 and with an energy density of 12.46 W h kg−1. The MnSe(20)/NiCo2O4 asymmetric cell showed excellent long term cycling stability for 5000 cycles having a capacitive retention of 86%.