Based on the Köppen climate classification, Mount Silverthrone is located in a subarctic climate zone with long, cold, snowy winters, and cool summers. Temperatures can drop below −20 °C with wind chill factors below −30 °C. This climate supports glaciers on it slopes including the Brooks Glacier. Precipitation runoff from the mountain drains into tributaries of the McKinley River, which in turn is part of in the Tanana River drainage basin. The months May through June offer the most favorable weather for climbing or viewing.