The northeastern state of Sikkim lying in central segment of the Himalayan orogen is a seismically active region which was plagued by the recent 2011 Mw6.9 earthquake. Analysis of local earthquakes recorded at the recently deployed seismic network of 27 broadband seismic stations revealed seismogenic zone extending down to lower crustal depths with a predominant strike-slip faulting mechanism. Persistent seismicity in a region with complex tectonic setting makes it imperative to study the site characteristics crucial for determining the local site conditions. Here, we harness the noise and local earthquakes records from the Sikkim network to compute horizontal-to-vertical spectral ratio (HVSR) for site characterization. Local geology and topography are observed to incite distinctly intricate trends in the HVSR curves. The thick sedimentary deposit of the Himalayan foreland basin causes high amplification (∼7) at low resonant frequencies (<1 Hz). The HVSR curves in the western section of Main Central Thrust Zone exhibits distinct double amplification peaks (∼2.5 at 1 Hz and 5 Hz) under the influence of the parallely dipping sheets of the duplex structure. Whereas, the eastern section of Main Central Thrust zone exhibit a rather irregular trend owing to its proximity to the transitioning lithological unit. The central section prone to landslides has characteristic peaks at 2 Hz and 8 Hz, indicative of the geometry of the sliding surface. Effects of towering topography and high wind speeds at corresponding elevations are observed to result in anomalously high amplification (∼25) at low frequencies (< 1 Hz). Directional amplification along discrete azimuth signifies the pronounced effect of topography and geometry of lithotectonic units in site response. Locally varying site response with prevalent seismicity amplifies the seismic hazard risk potential of Sikkim Himalaya.