Yushima Seido

Yushima Seido (湯島聖堂), which is a temple of Confucius, was established in 1632 as a private shrine and was relocated here in 1690 as a facility of the Tokugawa Shogunate. Confucian temples are rare in Japan, and among them this one is the most well-known.
Except for a few small exceptions, its buildings were reconstructed with concrete after they were destroyed by the Great Kanto Earthquake of 1923. Its architecture is built in Chinese-style so it's a little different from Shinto shrines or Buddhist temples.
Across the road from the precincts stands Kanda Shrine, so even though each of them is not so large, together they can be attractive, considering their accessibility - Yushima Seido is a 2-minute walk from JR Ochanomizu Station, which is two stations away from JR Tokyo Station.

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Kanda Shrine in Chiyoda-ku, Tokyo

The guardian of the town of Edo (present-day Tokyo).

Shibun-kaikan is the temple office.

Nyutokumon Gate is the sole building remaining from the feudal times.

Taiseiden is the main hall where Confucius and some other figures are enshrined.

The front door of Taiseiden is open only on Saturdays, Sundays & national holidays.

Holy Resurrection Cathedral

Holy Resurrection Cathedral in Tokyo, known briefly as Nikorai-do (ニコライ堂) in Japan, is the top cathedral of the Japanese Orthodox Church.
Its church building is the largest Byzantine-style architecture in Japan. It was built in 1891 and survived the 1923 earthquake and WWII, though heavily damaged by the earthquake. This construction is in pure European-style designed by European architects so it may not be what you expect to see here in Japan if you are a foreign visitor, but this place is also within a few minutes' walk from JR Ochanomizu Station so I decided to mention it a little.