Shafiqa Habibi is from an Ahmedzai Pashtun family from an upper-class background. Although she grew up in Kabul, her family is from Logar province. In 1966, Habibi obtained a degree in journalism from Kabul University. She is married to Mahmoud Habibi, who served in various positions in the Afghanistan government. These roles included information minister to King Zahir Shah, and president of the Afghan senate under President Mohammad Najibullah. When the Mujahideen took control of Kabul in 1992, she and her husband briefly moved to Mazar-e-Sharif, along with hundreds of thousands of others. When the United States began bombing Kabul in 2001, Habibi fled to the city of Peshawar, in Pakistan.