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The Secret of Platform 13? This doesn't ssssuper match your description but it has enough elements in common that I thought it might be worth a check!
Thank you for the suggestion, but that's not it! I do also have that book, thouhg. :)
Pendragon?
Thank you, but nope! I guess I should add that this book would have been available in the late 90s.
Gregor the Overlander maybe? that came out in the early 2000's though, and only fits your description a little bit.
Edited by donatello-is-the-fellow what the fückkkk you have to fucking BÜCKLE uuuup its the LAW
I recall reading a book as a child that was about a pair of children that entered a magial world through an abandoned subway station. They had tokens that they used to pass through. They befriended amagical creature that I think was a giant turtle or caterpillar that I believe died later in the story? Based on vague memories of how the library was layed out, I would guess it was aimed at 10-13 year olds.