It is essential to understand the soil characteristics of the subsurface layers for any engineering construction. In difficult terrains like hilly areas, conventional methods of investigation are expensive and difficult to conduct. It calls for nondestructive testing methods to get reliable estimates of subsurface properties. In the present study, seismic refraction tomography (SRT) technique and multichannel analysis of surface waves (MASW) methods were carried out along five selected profiles in Phuentsholing region of Bhutan Himalaya. The profile length ranges from 37 to 81.5 m, and depth of imaging down to 10 m. While the SRT data imaged the P-wave velocity (Vp) structures, the MASW imaged the shear wave velocity (Vs) structures. The P-wave images provide a fair knowledge of geological layers, while the MASW images provide S-wave velocity structures (Vs). These results are useful to estimate soil parameters, like the density, Poisson’s ratio, Young’s modulus, shear modulus, N-value and the ultimate bearing capacity. The seismic images reveal the presence of sand, sandy clay, gravels and shale layers below the selected sites. Bhutan Himalayas being seismically vulnerable, the obtained results in terms of shear wave velocity were accustomed to categorize the sites as per NEHRP site classes, and a ground response analysis was performed to determine the reliable amplification factors. From the study, it is suggested that the engineering construction is feasible at all the sites except in one site, where an indication of saturated soil is observed which is vulnerable for liquefaction, and ground needs to be improved before construction at that site.