As a promising non-precious catalyst for the hydrogen evolution reaction (HER; refs 1-5), molybdenum disulphide (MoS2) is known to contain active edge sites and an inert basal plane. Activating the MoS2 basal plane could further enhance its HER activity but is not often a strategy for doing so. Herein, we report the first activation and optimization of the basal plane of monolayer 2H-MoS2 for HER by introducing sulphur (S) vacancies and strain. Our theoretical and experimental results show that the S-vacancies are new catalytic sites in the basal plane, where gap states around the Fermi level allow hydrogen to bind directly to exposed Mo atoms. The hydrogen adsorption free energy (ΔGH) can be further manipulated by straining the surface with S-vacancies, which fine-tunes the catalytic activity. Proper combinations of S-vacancy and strain yield the optimal ΔGH = 0 eV, which allows us to achieve the highest intrinsic HER activity among molybdenum-sulphide-based catalysts.