I took a look at the JR Pass website, but it's not very specific when it comes to dual citizens. My child has Canadian and Japanese citizenship and both passports.
Current the child is under 6, so they don't need a JR Pass, but once the child is over 6, I'd need to get a child JR Pass.
From other questions, I've understood that you're supposed to use the Canadian passport at the airline (so it matches the ticket), and the Japanese passport at immigration points when entering and exiting Japan.
In the past when I've gotten a JR Pass for myself, I've had to show my Canadian passport with the stamp from immigration, but my child won't have that if they use the Japanese passport. This website seems to state that the dual citizen should use the non-Japanese passport, but I can't find anything on the official website, plus this goes against what I've heard for entering Japan.
I've seen the changes from 2017 that say Japanese nationals who have lived abroad over 10 years can use a Japanese passport, but as the child is under ten years old, I'm guessing this doesn't apply?