Others include rampant poverty, harassment and the government's failure to make education spending a priority. Both sexes have suffered from the lack of funding, but girls, who have somewhat lower rates of literacy and school attendance, are in a particularly perilous position.
The Oct. 9 attack on 15-year-old Malala Yousufzai, who is hospitalized in Britain, showed that the barriers to girls' education are highest in Pakistan's northwest, where the Taliban are strongest. The militants have blown up hundreds of schools and kidnapped and shot education activists like Malala.
The need for education is stark:
— Only 40 percent of Pakistani girls 15 or younger are literate, according to the United Nations.
— Roughly 50 percent of girls are enrolled in school, according to a report by the Society for the Protection of the Rights of the Child.
— Only one in five students is female in the semiautonomous tribal region along the Afghan border, the Taliban's main sanctuary in the country, according to the U.N.
The Taliban and their allies are opposed to education that isn't rooted in their hardline interpretation of Islam and object to women working outside the home or traveling without a male escort.
Militants destroyed or damaged at least 943 schools in the tribal region and Khyber Pakhtunkhwa province from 2009 to 2011, according to Pakistani government figures.
Some were targeted because they were used by the military, but many of the attacks were motivated by the Taliban's opposition to girls' education and schooling that doesn't follow their strict interpretation of Islam.
"The Taliban have scared people," said Hamid Ullah Khan, a teacher from Lower Dir in Khyber Pakhtunkhwa. "This is also one of the main reasons that women are not studying at schools in good number."
The government has worked with the international community to rebuild some of the schools targeted by the Taliban. But the attacks dealt a blow to an education system that was already in shambles across the country, in part because of the low level of government spending.
The education crisis is apparent in the schools' infrastructure. Only 39 percent of schools have electricity, and only 62 percent have bathrooms, according to the Society for the Protection of the Rights of the Child.
Many Pakistani families are struggling to make ends meet, and if they have money for books, school uniforms or private school tuition, they often prefer to spend it on education for one of their male children.
Bismillah Jan, a teacher from Mir Ali town in the North Waziristan tribal area, said most parents were happy to send their daughters to school, but many had large families and simply couldn't afford to send everyone.
Many families in conservative areas of the northwest and elsewhere in the country worry about sending their daughters to school because they might be harassed on the way or when they arrive. Many also oppose their daughters having male teachers. The lack of bathrooms, especially separate facilities for girls, deters many parents who don't want their daughters to have to relieve themselves in a field.
Groups that have had success in educating girls say they have focused on those parental concerns.
The Karachi-based Citizens' Foundation is a non-profit institution that has built 838 private schools across Pakistan, including more than 100 in Khyber Pakhtunkhwa and southwest Baluchistan province, both conservative areas of the country with generally low female enrollment. About 50 percent of their students are women, according to statistics on their website.
A former vice president for the organization, Ahson Rabbani, said the organization builds schools close to the community so students don't have to travel far to get there and constructs separate toilets for girls, boys and teachers. The schools are surrounded by a wall with a guard out front, and all the teachers are women from the same community as the students.
Girls who get an education are more likely to send their own daughters to school when they grow up and have children, said Ghulam Zakia, principal at a government girls' school in the city of Rawalpindi, near the capital, Islamabad.
When Zakia became principal 33 years ago, she had to actively lobby parents to send their daughters to the school, which has focused on building ties with the local community and hiring good female teachers. Now the school is so popular that even parents of some boys push to send their children there, forgoing the nearby government boys' school.
Abdullah Khan in Dir and Rasool Dawar in Peshawar contributed to this report.