JR East's Ochanomizu station lies next to the Kanda River. During the Edo period, the Kanda River was rerouted to pass through Ochanomizu, which was otherwise a highland between two valleys. Hijiribashi (聖橋, also known as Hijiri Bridge, Hijiribashi Bridge) crosses over the river near a station exit. The subway Marunouchi Line makes a short above-ground appearance as it passes over the river. Holy Resurrection Cathedral (Nicholai-dō) is easily accessible from the Hijiribashi Exit of this station. The Ochanomizu neighborhood is known for its many guitar and instrument shops.
The JR East portion of the station has two island platforms serving four tracks. Tracks 1 and 4 (the outer tracks) serve trains on the Chūō Line (Rapid) whilst tracks 2 and 3 are used by trains on the Chūō-Sōbu Line.
There are two exits from Ochanomizu to street level. The larger of the two is the Ochanomizu-bashi exit on the western end of the station which features ticket vending machines, a JR reservation office, toilets, and lockers. The other is the Hijiri-bashi exit which only has ticket vending machines and bathrooms.