I’ll be studying in Tokyo for 2 years, and I figure it would be economical to get a student commuter pass. I was wondering if it’s possible to get a student commuter pass that can cover stations from different train companies?
For example, the station nearest my school is along the Tokyo Metro lines, but the station nearest my where I’m going to live is not along the Tokyo Metro lines.
Yes, if you buy a commuter pass it will cover the entire route between the target stations. For example, if you live in Shinjuku and go to school in Yokohama, you can get a pass that covers Shinjuku-Shibuya (JR line) and Shibuya-Yokohama (Fukutoshin subway line).
The good news is, you can also get on and off at all the stations in between, so you can use the pass on your free days to go hang out, and it doesn’t cost you more! 
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