Child marriage, a lack of female teachers and poor school facilities are also making girls miss out on education.
Almost half of all children in Afghanistan are missing out on school - and girls are bearing the brunt because of poverty and discrimination.
In the worst-affected areas as many as 85% of girls are not getting an education, with child marriage, a lack of female teachers and poor school facilities among the major reasons.
60% of the 3.7 million children and youth aged from seven to 17 who are out of school are female, according to a new report. It is the first time the out-of-school rate has increased since 2002.
"Business as usual is not an option for Afghanistan if we are to fulfil the right to education for every child," said Adele Khodr of UNICEF in the report conducted by the United Nations children's agency, USAID and an independent think-tank.
"When children are not in school, they are at increased danger of abuse, exploitation and recruitment."
Khodr said that while the numbers are concerning, there is also progress and hope. School dropout rates are low and 85% of boys and girls who start primary school go on to complete the last grade - while 94% of boys and 90% of girls who start lower secondary also complete the grades.
She said the challenge is to get children to start school in the first place.
"We commend the government of Afghanistan for prioritising and declaring the year 2018 as the year of education," said Khodr.
"Now is the time for a renewed commitment to provide girls and boys with the relevant learning opportunities they need to progress in life and to play a positive role in society."
The report said the reasons for so many children missing out on education include the ongoing conflict and worsening security situation, combined with deeply engrained poverty and discrimination against girls.
The worst-affected provinces include Kandahar, Helmand, Wardak, Paktika, Zabul and Uruzgan, where up to 85% of girls are not going to school.
The report said action by government and civil society was needed to address the challenges. It said early learning opportunities and community-based education could help to tackle problems facing girls, such as harassment on the way to school.
As well as protecting children and schools from harm, the report called for four major actions:
- Target provinces with disproportionately high rates of out-of-school girls, including working with religious leaders and other groups to advocate for increased education
- Ensure girls' learning facilities meet basic security and health standards, including toilets, handwashing facilities and safe drinking water
- Recruit and build the capacity of female teachers
- Address child marriage
Education of children is the most important tool in fighting war, poverty and unemployment.
At a seminar in the capital Kabul to launch the report, Afghan education minister Mirwais Balkhi told a seminar there were "many reasons" for children not going to school.
He did not specifically mention the Taliban or Islamic State, who are opposed to education for girls and have forced the closure of dozens of schools.
Balkhi said: "Education of children is the most important development in all human communities. It is the most important tool in fighting war, poverty and unemployment."
Teenage girl Ziwar, from central Daikundi, one of the safest provinces in the country, told the seminar she had been at school until she was 14.
She said: "I can read and write. I can write a letter. I learn from books.
"I want to continue my studies. I want to become a doctor in the future."