The City of Panabo, being a part of Davao Province, experienced the same climatic condition. The province has type IV climate under the coronas classification and is characterized by unpronounced dry and wet seasons. Rainfall is more or less evenly distributed throughout the year with no pronounced rainy and dry season. It is located at the south of the typhoon belt therefore the occurrence of typhoons is minimal. It also naturally protected by mountain ranges that act as barriers from the onslaught of typhoons. The El Niño phenomenon, a recurrent and global climatic abnormality that appears every 2 to 7 years is said to be triggered when the strong westward blowing trade winds weaken and reverse direction. This generally leads to prolonged dry season and excessive rainfall in short periods that can cause widespread flooding in low-lying areas. Compared to other provinces in Region XI and in the Mindanao area, Davao del Norte has demonstrated a low degree of vulnerability to various El Niño episodes.

The fairly pronounced rainy months in the province are from November to February. The total rainfall, which was recorded at 3,031.6 mm in 2000, is the highest in the past twenty years. The province experienced a very high rainfall of 433.4 mm last February 2006. The volume of rainfall varies from 1,354.0 mm to 3,031.60 mm per year. The monthly average rainfall is 112.84 mm for minimum and 252.63 for maximum. There are two prevailing wind directions in the city. From, January to April, the predominant wind direction is Northward from Davao Gulf where the cool air of the sea replaced the warm air mass over the city. From May to December, the prevailing wind direction is southward from Davao Gulf with 3.6 Kph maximum wind velocity.