She was welcomed back by Afghan President Ashraf Ghani in Kabul on Wednesday, a presidential spokesman told CNN.
Photographs released by the Afghan presidential office show Gula, in blue, and other family members standing and talking with the President.
Gula, whose striking green eyes in a National Geographic cover photo made her face known around the world, was 12 when photographer Steve McCurry captured his iconic image of her living in a refugee camp for Afghan nationals in Peshawar.
Now in her 40s, she was arrested in the same city last month for falsifying documents and illegally staying in Pakistan.
Speaking to CNN last week from a hospital in Peshawar, where she was receiving treatment for a medical condition, Gula said: "I want to go back to Afghanistan, to my hometown."
She pleaded guilty to the charges of illegally staying in Pakistan and was sentenced to 15 days in jail and fined, her lawyer Mohsin Darwar, told CNN.
The sentence took into account the fact she has Hepatitis C, the condition for which she is receiving treatment, according to Mubashir Nazar, another lawyer representing her.
Nephew: 'She never understood her fame'
Gula's nephew, Neimat Gul, told CNN that his aunt had never understood the attention she had received in response to the famous magazine cover.
"She is very innocent. She never understood her fame, or the reason for it, which is why hasn't capitalized on it," he said. "Otherwise she would not be in situations like this."
Amnesty International last week condemned the decision to deport Gula, calling it a "grave injustice."
Human Rights Watch said since July 1, Pakistan has repatriated 370,000 Afghans, nearly 220,000 of them registered refugees.
"They are joining more than 1 million internally displaced Afghans who are struggling to survive in a country still wracked by conflict and crushing poverty," the group said in a statement.