I'm not sure of the exact grammatical explanation, but it's correct. The first clause refers to the subject, however it comes before the subject, which can be a little confusing. You can think of it as having an 'understood' subject and verb in the first clause, if that helps make it clearer.
Although (he was) happy in the new school, he missed his friends"
Similar examples:
Although tired, they finished the marathon.
Although intelligent in general, he was stupid when it came to relationships.