Phuentsholing features a humid subtropical climate (Köppen classification Cwa). Because of its low elevation compared to the rest of Bhutan, it experiences significantly warmer temperatures year-round.
Summers (June to September) are hot, highly humid, and dominated by the South Asian monsoon, which brings torrential rainfall. Temperatures frequently reach 32°C (90°F) or higher during these months. Flooding and landslides along the highway are common natural hazards during the monsoon. Winters (December to February) are mild, dry, and pleasant, with average daytime temperatures around 20°C (68°F), making this the most comfortable time of year to visit. Snowfall in Phuentsholing is virtually nonexistent.