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The information was disclosed by a foundation run by Denis Mukwege, a Nobel laureate and gynaecologist on Tuesday, according to Aljazeera.
The Panzi Foundation charity hospital in Bukavu city said the children were admitted last month "in a state of suffering and psychological stress".
The 30-year-old alleged attacker was arrested in late April, civil activist Julien Namegabe told the AFP news agency.
The victims came from different families and ranged in age from eight to 15.
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The suspect "bought their silence with small gifts for several weeks", according to the Panzi Foundation.
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Evariste Kajibwami, a clinical psychologist who has been following the boys since their admission to the hospital, said on the foundation's website that they "presented a mixture of sadness, fear and shame".
The foundation said it would help the victims "until justice was done".