Methenamine, a urinary antiseptic with antimicrobial properties, decomposes into toxic formaldehyde under acidic conditions. Its use is prohibited in dairy cattle in Korea to prevent harmful residues in milk. This study was designed to develop and validate a sensitive and reliable LC–MS/MS method for determining methenamine in raw milk and bovine muscle in compliance with the Positive List System (PLS) regulations. Samples were extracted with acetonitrile (ACN)–methanol (MeOH) (7:3, v/v) containing ammonia water, followed by defatting with n-hexane and purification with primary secondary amine (PSA). Chromatographic separation was performed on a hydrophilic interaction liquid chromatography (HILIC) column, and quantification was conducted using matrix-matched calibration to minimize matrix effects. The method showed excellent linearity (R² > 0.999), low limits of quantification (LOQ) (0.49 μg/kg for raw milk; 0.64 μg/kg for bovine muscle), and acceptable recoveries (78.1–102.8%) with precision (CV ≤ 8.75%), meeting Codex CAC/GL 71-2009 criteria. Stability studies demonstrated that methenamine remained stable in stock solutions, working standards and processed extracts under the storage and handling conditions used. Application to incurred samples resulted in the detection of methenamine in 2 of 32 raw milk samples (0.65 and 1.14 μg/kg) but in none of the 25 bovine muscle samples, with all detected levels below the Korean PLS limit. These findings confirm that the developed method is accurate, sensitive, and applicable for routine surveillance of methenamine residues to ensure consumer safety.