Ahmed's parents had been students in the United States in the 1990s, where his mother Aafia Siddiqui earned a PhD in cognitive neuropsychology. While living in the US his parents started a charity. They would later be identified as suspected terrorists. Ahmed and his younger sister were born in the USA, and lived there until 2002, when his parents returned to Pakistan, and their marriage broke up. Aafia was pregnant when the marriage broke up, and his younger brother was born in Pakistan in late 2002 or early 2003.
After the marriage broke up Aafia made a trip back to the United States, to look for an academic job. In March 2003 Aafia and all three children were living with relatives in Karachi, Pakistan.
Aafia and all three children disappeared during a trip to Karachi airport on March 23, 2003. Aafia's relatives went on record with their belief that her ex-husband's denunciations had led to the capture of Aafia and her children by security officials, and that they were being held in secret prisons. Her ex-husband claimed she was at large, living underground, as a ploy to prevent him getting access to his children.
According to the Arab News Pakistan's President, Asif Ali Zardari, had personally requested Afghanistan's President Hamid Karzai return Dr Aafia's children to their family in Pakistan.
In the summer of 2008 Aafia and a teenage boy were reported to have been apprehended by Afghan police. It was later confirmed that the teenage boy was her eldest son Ahmed.
On August 26, 2008 The United States State Department confirmed that the youth captured with Aafia Siddiqi on July 17, 2008 was her son, American citizen Ahmed Siddiqi.
Ahmed was transferred to the custody of Pakistani security officials. Joanne Mariner, Director of Human Rights Watch, criticized Afghanistan officials for transferring Ahmed to Afghanistan's National Directorate of Security—the NDS due to its reputation for using torture as an interrogation tool. Mariner pointed out that under both Afghan law Ahmed was too young to be held criminally responsible.
Ahmed was returned to the custody of his maternal family, while his mother was taken to New York City to stand trial for attempted murder. The whereabouts of Ahmed's younger siblings remained a mystery. During her interrogations following her 2008 arrest Aafia described visions of her youngest son as an angel, as he had died in custody with her during the period 2003-2008.
When a girl who may have been his younger sister Maryam was returned to the Ahmed's family, tests to confirm her identity were inconclusive. His aunt Fawzia expressed doubt that the girl was her niece Maryam. The Daily Times reported that the girl was only able to speak English and Dari, a dialect of the Persian language, and that when Ahmed was returned he too could only speak English and Dari.
In late August 2010, British journalist Yvonne Ridley, who had first reported that Aafia and her children had been held in the Bagram Theater internment facility reported that she had acquired a statement taken from Ahmed in 2008. She reported that the statement was taken from Ahmed by an American official when he was released.
The statement is the first from Ahmed. The statement is the first to appear to confirm Aafia's dream that her youngest child was dead. The statement, as quoted by Ridley, read: