The entrance to Meiji Shrine South Gate is a three minute walk from Harajuku Station. Exit Harajuku Station, and turn right. Follow the path for about one minute, until your reach a large concrete bridge that crosses the tracks of the Yamanote Line. Cross the bridge, and on your right hand side you will see a torii gate shrouded by trees. This is the entrance to Meiji Shrine. Alternatively, Meiji Shrine South Gate can be reached from Meiji Jingu Mae Station. Take JR Exit 2, leave the elevator, and the entrance to Meiji Shrine will be directly in front of you.
From Tokyo Station to Harajuku Station:
Take the Yamanote Line direct to Harajuku Station (30 minutes, ¥170)
From Shinjuku Station to Harajuku Station:
Take the Yamanote Line direct to Harajuku Station (4 minutes, ¥140)