Bilirubin (BR) is a product of hemoglobin breakdown, and its increasing levels in the blood may indicate liver disorders and lead to jaundice. Kernicterus is most dangerous in newborns when the unconjugated BR concentration can quickly rise to toxic levels, causing neurological damage and even death. The development of an accurate, fast, and sensitive sensor for BR detection will help reduce diagnostic time and ensure successful treatment. In this study, we propose a new method for creating a surface-enhanced Raman scattering (SERS)-active substrate based on gold-decorated silicon nanowires (Au@SiNWs) for sensitive label-free BR detection. Gold-assisted chemical etching of crystalline silicon wafers was used to synthesize SiNWs, the tops of which were then additionally decorated with gold nanoparticles. The low detection limit of model analyte 4-mercaptopyridine down to the concentration of 10–8 M demonstrated the excellent sensitivity of the obtained substrates for SERS application. The theoretical full-wave electromagnetic simulations of Raman scattering in the Au@SiNW substrates showed that the major contribution to the total SERS signal comes from the analyte molecules located on the SiNW surface near the gold nanoparticles. Therefore, for efficient BR adsorption and SERS detection, the surface of the SiNWs was modified with amino groups. Label-free detection of BR using amino modified Au@SiNWs with high point-to-point, scan-to-scan, and batch-to-batch reproducibility with a detection limit of 10–6 M has been demonstrated. Artificial urine, mimicking human urine samples, was used as the matrix to get insights into the influence of different parameters such as matrix complexity on the overall BR SERS signal. The signal stability was demonstrated for 7 days after adsorption of BR with a concentration of 5 × 10–5 M, which is the required sensitivity for clinical applications.