Transition metal dichalcogenides (TMDCs) based materials are considered as highly active alternatives to the precious Pt‐based catalysts for the hydrogen evolution reaction (HER). In particular, MoSe2 emerges as a promising catalyst due to its abundance and electrochemical stability, but further modifications are still required to enhance its performance, specifically in alkaline conditions. Here, we developed a method to obtain MoSe2 with two cobalt doping patterns: homogeneously doped and edge doped nanoflowers, with abundant edge sites and extended surface area. The results show that low concentration of doping enhances the catalytic activity toward HER. Incorporation of cobalt as a substituent dopant within the layered structure of MoSe2 appears to have two major contributions: it changes the chemical environment providing more active sites with favored hydrogen adsorption properties, and improves the charge transfer resistance and thus facilitates the HER kinetics. Moreover, the homogeneous and edge‐doped nanoflowers show different pH‐dependence of HER activity. Edge‐doped samples exhibit significantly improved performance in acidic medium, while the overpotential increases in alkaline environment upon doping. A mechanistic explanation of the observed effect is proposed. This work opens up an additional path for improving the catalytic activity of TMDCs in acidic or alkaline medium using a simple and facile method with only small quantities of dopants.