Khonsa features a subtropical highland climate (Köppen: Cwb/Cwa), heavily influenced by its elevation and the Indian monsoon. The town enjoys a relatively temperate climate year-round compared to the sweltering plains of neighboring Assam. Summers (April to June) are mild and pleasant, with average temperatures ranging from 15°C to 25°C. Winters (November to February) are quite cold, with temperatures frequently dropping between 5°C and 15°C, though snowfall is extremely rare.
The region experiences a prolonged and intense monsoon season from June to September. Rainfall is heavy and persistent, often triggering landslides that can temporarily isolate the town by cutting off road access. Humidity remains high throughout the wet season. The best time to visit Khonsa is during the dry months, from October to April, when the weather is crisp, the skies are clear, and traditional festivals are in full swing.

