The Gorakhpur city experienced several high-intensity tremors because of ongoing seismic activities in the Himalayan region. Therefore, the characterization of its subsurface is crucial for a better assessment of the seismic hazards. Ambient noise measurements at 360 sites single-station and four array sites show the predominant frequency peak varies between 0.434 to 1.02 Hz from horizontal-to-vertical spectral ratio (HVSR) analysis and amplitude increasing toward the north with maximum amplification is 4.81. The structure of the shallow soft soil has been observed by frequency wavenumber (F–K) analysis. Joint inversion of the HVSR and Rayleigh wave dispersion curves reveals three layers of soft, dense and stiff soil sediments of varying thickness. The shear wave velocity (Vs) of the sediment varies between 280 to 1200 m/s from top soil to 100 m subsurface depth. The observed Vs models correspond to soil classifications ranging from soft soil to very dense soil and rock.