Nobody hands you a rulebook when you step onto a Tokyo train, but everyone around you is quietly following one. Break it and you'll get a look, not a lecture - Tokyo doesn't do public scolding. Here's what took me years to absorb, condensed into one read.
THE BASICS
Phone calls are off-limits. Texting, scrolling, and gaming are all fine, but taking a call is one of the fastest ways to mark yourself as a tourist. If your phone rings, either silence it or step off at the next stop. Most locals keep their phones on silent mode (manner mode) as a default.
Talking is kept low. Trains in Tokyo are quiet by default - not silent, but hushed. Save the loud conversation for the platform or the izakaya afterward.
Let people off before you board. This sounds obvious, but rushing the doors is one of the most common mistakes visitors make. Stand to the side, let the train empty, then step in.
PRIORITY SEATS
Every car has a marked section, usually near the ends, reserved in spirit for elderly passengers, pregnant women, people with disabilities, and parents with small children. You're allowed to sit there if it's empty, but the expectation is that you give it up the moment someone who needs it steps on - and that you switch your phone to silent near these seats, since Japan still takes old pacemaker-interference guidance seriously even though the science has moved on. You'll notice regulars quietly stand up before they're even asked.
RUSH HOUR SURVIVAL
Weekday mornings between roughly 7:30 and 9:00, and evenings from about 5:30 to 7:30, are not the time to be precious about personal space. Trains get pushed to capacity, sometimes with station staff physically assisting the doors closed. If you can avoid these windows, do - Tokyo is a different, much calmer city outside of them. If you can't, keep your bag in front of you, hold on to something, and accept that you'll be closer to strangers than you've ever been by choice.
Some lines run women-only cars during rush hour, marked clearly on the platform and the train itself with pink signage. They exist to cut down on groping incidents, which unfortunately still happen in packed cars - respect the boundary if you're not meant to be in one.
ESCALATORS
Stand on one side, walk on the other - in Tokyo, that's stand left, walk right, the reverse of Osaka's stand-right convention. It's not written down anywhere, but everyone follows it, and standing on the wrong side gets you gently but firmly nudged. If you're not in a hurry, just stand - Tokyo has slowly been pushing a stand-on-both-sides safety campaign, but old habits move slower than trains.
MY TAKE
None of this is about being perfect - visitors get a pass for plenty. But the phone call rule and the letting-people-off rule are the two that actually annoy people, so if you only remember two things, make it those. Everything else, you'll pick up naturally by watching the person next to you and quietly doing what they do.