Waste liquid mercury generated as a by-product of the Merrill–Crowe process in gold mining and recovered from mercury-containing waste must be stabilized for secure storage or disposal. This study developed a procedure for mercury stabilization. A ball mill with a 0.5 m3 capacity and a rotational speed of 43 rpm was used to stabilize the residual mercury with sulfur. The treatments were conducted for 30, 60, and 90 min at mercury: sulfur molar ratios of 1.0, 0.8, and 0.67. The ball loading ratio was 7.0 with residual mercury, and the temperature was below 40 °C. The treatment efficiency was evaluated by measuring the concentrations of mercury and other metals using the Toxicity Characteristic Leaching Procedure (TCLP), examining the stabilized residual mercury by X-ray diffraction, and conducting bioassays on Daphnia magna and Lactuca sativa. Principal component analysis (PCA) was performed on the aforementioned variables. The 90-min treatment, with a mercury-to-sulfur molar ratio of 0.67, stabilized mercury mainly as cinnabar compared with the other treatments and presented leachate mercury values below the detection limit <0.003. The leachate from the treatments also showed values of 21.28–38.44 toxic units, classified as very toxic, and generated toxicity, particularly for D. magna, because of the presence of other metals such as Al, Ba, B, Ca, Cu, Cr, Fe, Mn, Ni, and Zn. The variability of the residues in the PCA analysis was explained by the treatment effect and the presence of other metals in the residual mercury. The stabilized residual mercury obtained was classified as non-hazardous and could be stored or disposed of as ordinary waste in a security landfill.