The tone of “The Sisters” is both childlike and formal. The unnamed narrator telling the story is simultaneously a naïve child and also a perceptive young person with a large vocabulary, leading to the somewhat contradictory tone. Take the following passage, for example, in which the narrator reflects on Old Cotter’s insinuations that Father Flynn was a pedophile:
Though I was angry with old Cotter for alluding to me as a child I puzzled my head to extract the meaning from his unfinished sentences. In the dark of my room I imagined that I saw again the heavy grey face of the paralytic. I drew the blankets over my head and tried to think of Christmas.
The tone here is complex. On the one hand, the narrator’s formal vocabulary implies that he is responding to Old Cotter’s criticisms of his teacher in a mature way (as seen in language like "I puzzled [...] to extract the meaning from his unfinished sentences"). On the other hand, his childish frustration with being referred to as a child and his youthful decision to hide in bed and "think of Christmas" gives this passage a more immature tone.
It is notable that, in the second half of the story, the narrator essentially disappears as Joyce switches his focus to capturing dialogue between the three women in the story (the narrator’s aunt and Father Flynn’s two sisters) at the priest’s memorial service. Here, the tone becomes contradictory in a new way, as the women speak of the priest in simultaneously reverential and concerned ways. This is Joyce’s way of highlighting the hypocrisy of practicing Catholics in Dublin: they see the issues with the Church clearly (the women note how, by the end of his life, Father Flynn had gone mad) yet speak of such issues in hushed tones rather than holding the Church accountable.