Activists said the girl appeared in court after being taken to a women's shelter for safety from her own family, who had threatened to kill her for bringing "dishonour" on them.
The sentence, passed by a court in Kabul on Saturday, came just weeks after five men were hanged for the gang-rape of four adult women.
Hasina Sarwari, the head in Kunduz province of the Women for Afghan Women (WAW) non-government organisation, said the student at a mosque school was raped in May by Mohammad Aminullah Barez, who taught the girls religious studies.
She first tried to hide what had happened to her but was later admitted to hospital for bleeding, where doctors discovered the rape. He was arrested by police later.
"We are happy for the court's decision but we wanted him to be executed," Sarwari told AFP. Her organisation supported the girl in her case and gave her shelter in Kabul.
"After the rape happened the family of the girl wanted to kill her out of shame, even the nurses were not ready to treat her when she was bleeding in the hospital," she said.
"They would shout 'May you die, you brought disgrace to our family!' and 'We will kill you and dump your body in the river'.
"We got scared too, but we somehow managed to sneak her out of the hospital and take her to a WAW shelter," she added.
The girl was later brought to Kabul where she was treated for genital injuries and kept in a women's shelter before she appeared in court.
Benafsha Efaf Amiri, another member of the WAW, said that although the cleric had admitted having sex with the girl, he tried to persuade the court it was consensual and he should therefore only receive 100 lashes as punishment.
Judge Sulaiman Rasouli rejected that argument because it would entail lashing the girl too and treating her as an adulterer rather than a rape victim.
Amiri hailed the verdict as a victory for Afghan women, who still face violence despite reforms since the fall of the hardline Islamist Taliban in 2001.
"Our assessment from yesterday's court session has made us optimistic for ensuring justice and for ensuring the rights of women of Afghanistan," she said.
It was also termed a "just verdict" by the Women's Affairs ministry in a statement to the media.
Amin's lawyers are expected to appeal to try to reduce the sentence.
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Per CNN ... "What's striking about this case is not that it happened, but that a 10-year-old girl found the courage to speak up -- and that authorities didn't charge the child herself for a moral crime." That tells you how much Islam has to evolve - women/children have rights.
So it was the age that saved the girl from punishment. Had she been a bit older, 14, 15 or 16, than she would do the 'crime' too, if she wasn't killed by her family already. What a sick society!
"Judge Sulaiman Rasouli rejected that argument because it would entail lashing the girl too and treating her as an adulterer rather than a rape victim."
Hats off to this judge. Looks like Afghans have better understanding of religion than muslims in Pakistan and all its institutions.
Mullahs are same everywhere.They add their own agenda to religious studies.
She was admitted to a seminary to learn Islamic studies. Even the cleric don't believe in Islamic studies. It is only to satisfy their lust, girl students are admitted. This girl is bold enough to expose him. But how many girls silently weeping being raped by this priest.
Hats of to Kabul court. I wish justice would prevail in Pakistan too where my rapest is still roaming free