The boy, who lives in the north of England, was not formally arrested or charged, police said. However, they said that his details would be stored for at least 10 years on the police database.
The information could also be disclosed to future employers, according to his mother.
Police said the children were named in a crime report, but it was not in the public interest to prosecute.
The schoolboy, whose identification was not disclosed, said he took the naked photo of himself in his own bedroom.
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However, before the image could have disappeared, the girl saved it on her own phone and it was then sent to other pupils at the school.
"At no time was any young person arrested or interviewed under caution in a formal police interview," a statement from the investigating police force said.
"The report of crime has been filed with the children involved named and given an outcome of not in the public interest to prosecute," it said.
The names of those involved in such cases are stored in a system for at least 10 years for sex offences.