Tokyo Metro is operated by Tokyo Metro Co., Ltd. (????????? Tokyo Chikatetsu Kabushiki-gaisha?), a private company jointly owned by the Japanese government and the Tokyo metropolitan government.

The company replaced the Teito Rapid Transit Authority (????????? Teito Kosokudo Kotsu Eidan?), commonly known as Eidan or TRTA, on April 1, 2004. TRTA was administered by the Ministry of Land, Infrastructure and Transport, and jointly funded by the national and metropolitan governments. It was formed in 1941, although its oldest lines date back to 1927.

The other metro operator in Tokyo is the government of Tokyo, through the Tokyo Metropolitan Bureau of Transportation, which operates the Toei system. Metro and Toei trains form completely separate networks.

While users of prepaid rail passes can freely interchange between the two networks, regular ticket holders must purchase a second ticket, or a special transfer ticket, to change from a Toei line to a Metro line and vice versa.

Much effort is made to make the system accessible to non-Japanese speaking users:
Many train stops are announced in both English and Japanese. Announcements also provide connecting line information.
Ticketing machines can switch between English and Japanese user interfaces.
Train stations are signposted in English and Japanese (in kanji and hiragana). There are also numerous signs in Chinese (in simplified characters) and Korean.
Train stations are now also consecutively numbered on each color-coded line, allowing even non-English speakers to be able to commute without necessarily knowing the name of the station. For example, Shinjuku Station on the Marunouchi Line is also signposted as M-08 with a red colored circle surrounding it; even if a commuter could not read the English or Japanese station names on signs or maps, he or she could simply look for the red line and then find the appropriately numbered station on said line.

Many stations are also designed to help blind people as railings often have Braille at their base.

Tokyo Metro stations began accepting PASMO contactless cards in March 2007.

The Tokyo Metro is extremely punctual and has regular trains arriving less than five minutes apart most of the day and night. It does not however run 24 hours a day. Lines tend to stop service between midnight and 1:00am and commence again at approximately 5:00am.

Tokyo Metro indicated in its public share offering that it would cease construction once the Fukutoshin Line is completed. Some therefore expect that the line will be the final expansion to the Tokyo Metro network, although several lines such as the Hanzomon Line have yet to be completed as planned.