If you use the phrase “saying his prayer” the “his prayer” part implies that he only knows one prayer. He can never pray anything different. If he knows more than one but is only saying one right now, the correct phrase is “saying one of his prayers” or “saying a prayer”.
Technically, it should be singular “prayer” as the Muslim boy is saying his one prayer at one time, not many prayers.
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If he says one prayer, and then says another prayer after that, that is saying “prayers”. If he says one prayer now, and will not say another one until later today, then “saying a prayer” is correct.
But in English we are not very clear about what is “one prayer”. If you say “bless me, and bless my parents” is that not two prayers?