An electrochemical method for the determination of trace levels of mercury(II) ions using metallophthalocyanine (MPc) modified glassy carbon electrode (GCE) via click chemistry by differential pulse stripping voltammetry (DPSV) is described for the first time. In this report, the novel synthesized low symmetry alkyne terminated cobolt Phthalocyanine (CoPc) derivative was prepared and characterized using FTIR, MS, UV-Vis, Elemental Analysis and cyclic voltammetry. Operational parameters such as number of scan for grafting step, concentration of CoPc derivative for clicking solution, and scanning potential range were optimized. Under the optimum experimental conditions, the anodic peak current is proportional to the concentrations of mercury over a wide range of 0.1 to 0.8 mM with the lowest detectable concentration of 440 nM. The selectivity of the CoPc modified GCE via click chemistry towards mercury in the presence of potential interferents such as copper, lead, cadmium and zinc was well studied. The fabricated electrochemical sensor exhibited very good electrocatalytic properties such as good reproducibility, stability and is suitable for the detection of mercury in tap water and seawater.