We studied the influence of a buried high‐velocity layer (HVL) on the surface ground amplification of the city of Llolleo, Chile, where large peak ground accelerations were observed during the 1985 8.0 Valparaiso and the 2010 8.8 Maule earthquakes. This study compares the theoretical and empirical surface response of a borehole seismic array located over a 60‐m depth soil deposit consisting of sandy and clayey soil layers with shear‐wave velocities () ranging from 200 to down to the bedrock and a 5‐m‐thick gravelly HVL at 21‐m depth. The seismic array is composed of accelerometers at the surface, the middle, and the bottom of the soil deposit, which allowed us to estimate the 1D empirical transfer function by computing spectral ratios from 16 earthquakes with magnitudes . The empirical spectral ratios between the surface and the bedrock show a complex seismic behavior characterized by four resonance frequencies with similar amplitudes between 2 and 10 Hz. We compared the empirical results with standard theoretical and experimental methods used in site characterization and found that the presence of the HVL in the city of Llolleo introduces complexities in the seismic behavior of the site that cannot be captured by individual standard methods.