Khan was born in Lahore and raised largely in Karachi, though her earliest years were nomadic and spent in Manila, Tokyo, and London. She received a scholarship to study at Hobart and William Smith Colleges, New York, from where she obtained a BA in Comparative Literature, and obtained an MFA from the University of Arizona, Tucson, US.
Khan's first novel, The Story of Noble Rot, was published by Penguin Books India in 2001, and reissued by Rupa & Co. in 2009. It was met with positive reviews in major periodicals and newspapers in Pakistan and India, and Khan was recognized as "a voice to watch out for."
Her second novel, Trespassing, was published simultaneously by Flamingo/HarperCollins in the UK and Penguin Books India in 2003. It has been translated into fourteen languages in eighteen countries. Set in the 1990s during the aftermaths of the Afghan War and Gulf War and completed a few months before 9/11, the book has been called "prescient" for how it illustrates the dark and troubled context of the west's involvement in the east and a precursor to the post-9/11 fiction from Pakistan that was to come. As Khan puts it "So much of this book is about history coming back to haunt you." Writing for Outlook magazine, Nilanjana S. Roy wrote that "While Khan's prose may be subtle, her style is as forceful as any of the great storytellers... Khan is creating a tradition and style of her own as a writer." Trespassing was shortlisted for the 2003 Commonwealth Writers' Prize, Eurasia region.
Khan's third novel, The Geometry of God, was printed by Rupa & Co. India in 2008. It tells the story of Amal, who, as a child, accidentally discovers the fossil of the ear of the first whale – or 'dog-whale', as she calls it – while on a dig with her paleontologist grandfather. Despite the pressures imposed on her by her family, and by society, Amal goes on to become the first woman paleontologist to work with men in the mountains of Pakistan to look for fossils of ancient whales. The novel was praised for boldly charting new territory, and for its characters. Khan was becoming recognized for her frank exploration of sexuality, unique in Pakistani English-language writing. Following its release in India, The Geometry of God was published in Spain, Italy, France, the US, the UK, and Pakistan. It won the Bronze Award for multicultural fiction in the Independent Publisher Book Awards, 2010; was selected as one of Kirkus Reviews' Best Books of 2009; and was a finalist of Foreword magazine's Best Books of 2009.
Khan's fourth and most recent novel, Thinner than Skin, was published in 2012 in the US, and subsequently in Canada, India, and France. It was nominated for the Man Asian Literary Prize 2012, the DSC Prize for South Asian Literature 2014, and won the inaugural KLF-Embassy of France Fiction Prize at the Karachi Literature Festival (KLF) in February 2014. In a joint statement, the jury explained its choice for selecting Khan's book for "The eloquent and elegant way in which she reveals a myriad of different worlds with masterly restraint. The novel animates mountains, lakes, wind and fire and other elements of nature that echo the complex emotions of her characters. Through the carefully structured plot and the well-wrought patterns of recurring images and incidents, emerge insights about homeland, belonging and dislocation, central to contemporary Pakistani life."
Khan's fiction has also appeared in numerous anthologies, including "Look, But With Love" (an extract from Trespassing) in And the World Changed: Contemporary Stories by Pakistani Women (The Feminist Press, 2008); "Ice, Mating" in Granta magazine's highly popular edition on Pakistan; "The Missing" in Tehelka magazine; and "The News at His Back" (an extract from Thinner Than Skin) in The Massachusetts Review.
In addition to her novels and short stories, Khan has published essays and articles around the world, including in Drawbridge UK, Dawn Pakistan, First City India, and for the online political journal, CounterPunch. Included in her articles for CounterPunch is her 2008 letter to Barack Obama, "Where's the Change, Barack?"The Story of Noble Rot (Penguin India, 2001. Reissued by Rupa & Co. in 2009)
Trespassing (Flamingo/HarperCollins UK, 2003. Metropolitan/Henry Holt and Company USA, 2004)
The Geometry of God (Clockroot Books/Interlink Publishing USA, 2009. Haus Publishing UK, 2010)
Thinner than Skin (Clockroot Books/Interlink USA, HarperCollins Canada, HarperCollins India, 2012)
2003 Trespassing was shortlisted for the Commonwealth Prize, Eurasia region.
2009 The Geometry of God was selected as one of Kirkus Reviews' Best Books.
2009 The Geometry of God was a finalist of Foreword magazine's Best Books.
2010 The Geometry of God won the Bronze Award in the Independent Publisher Book Awards.
2012 Thinner Than Skin was longlisted for the Man Asian Literary Prize.
2014 Thinner Than Skin was longlisted for the DSC Prize for South Asian Literature.
2014 Thinner Than Skin won the inaugural KLF-Embassy of France Best Fiction Prize.