"We were on the way to school when two men on motorbikes stopped next to us. One of them threw acid on my sister's face. I tried to help her and then they threw acid on me too," said Latefa, a 16-year-old student.
"We were shouting and people came to see what was going on, then the two men escaped," she said.
Latefa, who did not give her family name, was hurt and Shamsia, her 18-year-old sister, remains in a serious condition with acid burns across her face.
Girls were banned from attending schools under the Taliban government, which ruled Afghanistan from 1996 to 2001.
Women were also not allowed to leave the house without a male family member escorting them.
Al Jazeera's David Chater, reporting from Kandahar, said that Shamsia was in shock.
"She is shaking, and in extreme pain, and was not able to describe the event," he said.
"But Latefa, her sister, said that she is determined to continue her education, and she will not let this attack stop her from learning."
Chater also said that the school was empty, as students were afraid to attend classes.
The Afghan government condemned the attack, saying it was "unIslamic" and perpetrated by the "country's enemies", a usual reference to Taliban fighters.
"By such actions, they cannot prevent six million children going to school," the government said in a statement.
No one immediately claimed responsibility for the acid attack, and Qari Yousef Ahmadi, a Taliban spokesman, denied any involvement.
Bibi Meryam, Latefa and Shamsia's aunt, said that the family had not received any threats not to send their girls to school, but now they would consider keeping the girls at home until security stabilised.