Cherrapunjee is located on a plateau in the southern part of the Khasi Hills at a height of 1,484 metres above the sea level. Due to its location, it overlooks the plains of the neighboring country of Bangladesh. The valleys in and around the Cherrapunjee have subtropical forests as a result they are covered by lush green forests.

It has a subtropical highland climate. It receives both the southwest and northeast monsoonal winds due to which it has a single prominent monsoon season and is located on the Khasi Hills that increases the level of precipitation in the air.