Veterinary medicines are widely administered to farm animals since they keep animals healthy at overcrowded conditions. Nevertheless the continuous administration of medicines to farm animals can frequently lead to the presence of residues of veterinary drugs in consumption products. Amprolium is a quaternary ammonium compound used in the treatment of coccidiosis. In this paper, a method based on CZE to analyze residues of amprolium in eggs was developed and validated for the first time. Parameters such as electrolyte type, concentration, and pH were optimized. In order to improve sensitivity, field-amplified sample injection (FASI) was used for in-line preconcentration after a quick and simple sample treatment based on SPE (Envi-Carb). During method-validation studies using egg samples, a matrix interference was found at the migration time of amprolium. This compound was identified as thiamine and confirmed by MS(n) experiments using CE coupled to MS (CE-MS) with an ion-trap mass analyzer. CZE conditions were reoptimized to separate thiamine from amprolium allowing the quantification of amprolium in eggs at concentrations down to 75 μg/kg, which are far below the MRL-legislated values.