Sakena Yacoobi who has worked to rebuild education from the disruption of war, received the prize in the Gulf state of Qatar.
Her organisation, Afghan Institute of Learning, supported underground schools when the Taliban were in power.
Dr Yacoobi said the prize came at a time when people in Afghanistan were "suffering and feel hopeless".
Receiving the $500,000 prize (Â£324,000), Dr Yacoobi said: "It is particularly meaningful because this is such a crucial time in Afghanistan.
"My people live in terror and poverty."
The award was made by Sheikha Moza bint Nasser, chair of the Qatar Foundation, at the beginning of the annual WISE international education conference.
She said that Dr Yacoobi had been a "tireless advocate for the right to education" despite the "most adverse conditions of war and occupation".
"From refugee camps to secret night schools, and often at great personal risk, she established a network of organisations that provide general education as well as public health education."
The conference was also addressed by US First Lady Michelle Obama, who called for greater efforts to promote girls' right to education, and for equal respect.
"Solving our girls' education is definitely about resources but it is also about attitudes and beliefs," she said.
"It's about whether parents think their daughters are as worthy of an education as their sons. It's about whether our societies cling to outdated laws and traditions that oppress and exclude women.''
An Afghan girls' education campaigner has won the annual Wise Prize for achievement in education.