Tokyo’s train system is great but complicated. Here are the pitfalls I ran into…

Tokyo’s railway system is one of the most convenient ways to explore the city, offering extensive coverage and frequent service. Most travelers use a rechargeable “IC card,” which can be topped up with cash or—if you have an iPhone—through an app. At the moment, there’s no Android app and you can’t recharge the card with a credit card. The IC card isn’t always the cheapest option, but it is usually the easiest.

That said, visitors should be aware of a few quirks.

Tokyo’s trains are operated by several different companies, and each company manages its own lines. The IC card works by tapping in when you enter a station and tapping out when you leave. Because the system tracks where each trip begins and ends, using a paper day pass on one line and then switching to another can cause complications. There is no single day or weekly pass that covers all lines for one reasonable price.

If you enter the system using a line-specific day pass, you can’t switch to your IC card later because the gates won’t recognize where your journey started. You also can’t buy a ticket once you’re already inside the paid area. In these cases, you’ll need to speak with a station agent. They’ll determine your fare manually, but the amount can vary depending on how they interpret your journey.

For example, the Rinkai Line sells a day pass for 730 yen. Riding the entire line costs about 400 yen one-way, so taking it twice already makes the pass worthwhile.

If you exit a JR station after transferring from the Rinkai Line, you won’t be able to buy a ticket at the exit gates. You can try to use your IC card, but if the system can’t match your journey, you’ll need to speak with staff. Fares can range widely—from about 200 to 800 yen—depending on where they decide your trip began.

Whats the best way to get around this and save some money? If you have a pass and know you wont need to exit a rail line to get to your train buy the cheapest ticket 100-200 yen. You wont need it to exit because you have the pass.

Navigation can also be tricky. Google Maps is helpful but not always perfectly accurate. It may direct you to a platform without clearly indicating which direction you should board, and on many platforms trains run both ways. Loop lines can be even more confusing, as trains sometimes arrive at the same time on both sides.

The Rinkai Line connects directly to the JR Yamanote Line. In some cases the train continues onto the Yamanote tracks; in others, it terminates and all passengers must exit. This can vary depending on the time of day or the specific service.

Certain lines add to the confusion by looking very similar. The Keio Line and Musashino Line, for instance, overlap along parts of their routes and both use trains with red stripes. It’s surprisingly easy to board the wrong train and end up missing your stop.