I bought my niece a Kindle that just arrived and I'm about to load it up with books to give it to her tomorrow for her birthday. I've decided to be a sneaky uncle and include good books that can teach better abilities to think or at least to consider science cool and interesting. She is currently in the 4th Grade with 5th coming after the Summer.
She reads basically at her own grade level so while I'm open to stuffing the Kindle with books to be read when she's ready, I'd like to focus on giving her books she can read now. Ender's Game will be on there most likely. Game of Thrones will not.
What books would you give a youngling? Her interests currently trend toward the young mystery section, Hardy Boys and the like, but in my experience she is very open to trying new books with particular interest in YA fantasy but not much interest in Sci Fi (if I'm doing any other optimizing this year, I'll try to change her opinion on Sci Fi).
Since you said she's interested in fantasy, I'd suggest the Enchanted Forest Chronicles by Patricia C. Wrede (Dealing with Dragons is book one.) Unfortunately it's not on the Kindle yet, but it does a good job of pointing out common fantasy tropes in an entertaining way. Also, the main female character is a very good role model.
If you want more of a scientific mindset applied to fantasy, I'd say The Last of the Really Great Whangdoodles by Julie Andrews Edwards instills scientific curiosity very well. Also not available on Kindle...
Finally, (this time actually on the Kindle!) if you want to gently introduce her to sci-fi while still maintaining fantasy, Diane Duane's Young Wizard series is... decent. Might be a bit scary at parts, though. I don't recommend this as highly as the other two, though. It doesn't necessarily teach anything rationality (although it's been a while since I read it), it's just a good bridge into science fiction.
EDIT: I just thought of a great introduction to non-fiction reading. An Incomplete Education: 3,684 Things You Should Have Learned but Probably Didn't by Judy Jones. It's a general overview of a lot of topics ranging from history to philosophy to science, all in a humorous style. This was one of the books that kickstarted my love of learning when I was thirteen-ish.
I'd second the Young Wizards as an awesome read, although I wouldn't really call it sci-fi (or rational). More like fantasy with a thin jargon veneer. It's got strong protagonists of both genders and a very positive tone overall (I'm reminded of MoR!Harry saying 'If Light winning is a problem, let the Light win again')