Are both prepositions common? Is one better than the other?
The first thing children learn in/at elementary school is how to read and write Hiragana.
Google 'Ngrams' suggests that "learn in school" is relatively more common in AmE than in BrE, though both "in" and "at" are used in both varieties. This accords with my initial impression on reading the question. However, it's only a slight bias, and, for me, as a BrE speaker, though I would probably naturally use "at" myself, both "in" and "at" seem pretty much equally OK.
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Google 'Ngrams' suggests that "learn in school" is relatively more common in AmE than in BrE, though both "in" and "at" are used in both varieties. This accords with my initial impression on reading the question. However, it's only a slight bias, and, for me, as a BrE speaker, though I would probably naturally use "at" myself, both "in" and "at" seem pretty much equally OK.