Phuentsholing's topography is defined by its position as a border valley town. The town center is relatively flat, situated in the flood plain of the Amo Chhu at an elevation of roughly 290 meters (950 feet) above sea level.
From the town center, the land rises sharply. Neighborhoods like Rinchending and Kharbandi sit on steep hillsides overlooking the valley floor, reaching elevations over 600 meters. The lowest points are found along the southern riverbeds crossing into India. This rapid change in elevation creates a dramatic landscape but also poses significant challenges for urban planning and poses risks of landslides during the heavy monsoon season.

