This story can be described as being about the death of the imagination as one boy discovers the extent to which the imagination can make the most drab of settings magical and mysterious, and then experiences what happens when imagination vanishes and he is left with the crushing force of reality.
Perhaps the way in which setting and theme are most closely seen working together is through the description of the bazaar that the narrator finally reaches at the end of the story. Note the way in which, before he starts his journey, his imagination had painted an exotic and romantic picture of this bazaar as he imagines himself as completing a romantic quest for his lady-in-waiting:
The syllables of the word Araby were called to me through the silence in which my soul luxuriated and cast an Eastern enchantment over me.
The market itself becomes a powerful symbol of the speaker's imagination as he builds it up to be an Aladdin's cave of magic and mystery. However, when he makes his way there, the banal reality of the bazaar cannot be ignored:
I found myself in a big hall girdled at half its height by a gallery. Nearly all the stalls were closed and the greater part of the hall was in darkness. I recognised a silence like that which pervades a church after a service.
Instead of the golden enchantment he was expecting, the bazaar is actually characterised by darkness, silence and and an almost ominous feeling. It is this banal reality of the setting that results in the epiphany that the boy experiences, which makes him realise that he is a "creature driven and derided by vanity." Theme and setting link together to produce this conclusion.