Parasitic diseases have been the major source of concern and cause considerable losses in the freshwater aquaculture of India. Fish parasites proliferate quickly in favourable settings, compromising fish health and frequently resulting in high mortality. Identifying and implementing appropriate control techniques is the need of the hour to combat the diseases. Emamectin benzoate (EMB) is an efficient infeed therapy for ectoparasite control in fish. The aim of the present study was to determine the withdrawal period of EMB in silver carp (Hypophthalmichthys molitrix) commercially important fish species in southeast Asia. The depletion of EMB residues in silver carp muscle treated with a dose of 50 μg kg−1 body weight (BW) day−1 for seven consecutive days was assessed. Muscle tissue was sampled on the 7th day of EMB feeding and 1st‐, 3rd‐, 7th‐, 14th‐, 21st‐, 35th‐ and 41st‐day post‐medication (PM) for QTRAP 4000 LC–MS/MS analysis. The data revealed that the level of EMB in the fish muscle was 13.0 ± 0.1 parts per billion (ppb) on the 0th day of withdrawal. The residue levels were reduced significantly on the 3rd day, with traces of EMB recorded by 21st‐day PM and reached undetectable levels by 31st day PM. Considering the maximum residue limit (MRL) of 100 μg kg−1 for fish muscle, the present study's findings support the usage of EMB in silver carp under the conditions employed in the study. The current study provides crucial information on the use of EMB as an antiparasiticide in silver carp, considering the food safety issues.