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Salmonella Typhimurium is the prevalent pathogenic bacterium that causes foodborne-related diseases. Here, we developed a surface-enhanced Raman scattering (SERS) biosensor for S. Typhimurium detection. The biosensor was based on Au@Ag core-shell nanorods (Au@Ag NRs) to enhance Raman signal and aptamer-specific identification. 4-mercaptobenzoic acid (4-MBA) and aptamer-modified Au@Ag NRs were used as Raman signal probes. The aptamer adsorbed on the Au@Ag NRs surface when the reaction system was free of bacteria. Once S. Typhimurium was added, the aptamer then specifically identified and captured the cells. The decrease of free aptamers in solution restoring the SERS "hot spot" between the Au@Ag NRs and enhancing the 4-mercaptobenzoic acid (4-MBA) Raman signal. Quantitative analysis of S. Typhimurium was performed using Raman-enhanced spectroscopy. Under optimised conditions, the 4-MBA SERS intensity at 1072 cm−1 was used to determine S. Typhimurium in the range of 102–107 CFU mL−1 (y = 1660.84x+2340.7, R2 = 0.9912). The limit of detection was 64 CFU mL−1. This method also has high specificity and is not interfered by the other five control bacteria to complete the detection of S. Typhimurium. The developed method is simple, rapid, sensitive and specificity, which can be used to detect actual samples. It can be potentially used for detecting bacteria. • A novel aptamer based SERS assay for rapid detection of S. typhimurium was proposed. • The method is ultrasensitive for the detection of S. typhimurium with the LOD of 64 CFU mL−1. • The developed method showed good recoveries in real food samples contaminated with S. typhimurium. [ABSTRACT FROM AUTHOR]