The Muslim Mayor of London was asked “does it feel like coming home?” as he met local dignitaries in Wagah, on the Indian-Pakistan border.
The question was posed by BBC London reporter Karl Mercer on Wednesday as Khan stepped into Pakistan from India.
Watch the clip, which went viral on Twitter overnight, above.
Khan responded: “Home is south London mate.”
He continued: “But it’s good to be in Pakistan, it’s good to come from India - home of my parents and grandparents.”
The BBC said its reporter asked the question after local politicians suggested Khan’s visit was a “homecoming”.
Khan was born in Tooting, south west London, to Muslim parents of Indian heritage who settled as children in Pakistan with Khan’s grandparents.
Their move came amid Partition violence after the 1947 carving up by the British of Indian territory.
Massacres and killings took place as people of Muslim faith fled to Pakistan, while Hindus and Sikhs left for India.
His parents later moved to London in 1968, and Khan was born two years later.
The London Evening Standard reported that, speaking publicly about his family’s past, Khan said: “It was very difficult. My nan and that generation, their memories aren’t so great, because they remember what it meant.
“I was familiar with mates’ grandparents in Pakistan thinking unkindly towards the other faith, because their experience was the atrocities.”
Khan is undertaking the first ever trade mission by a London mayor to both India and Pakistan, despite reported hesitation from the Foreign Office.
Meanwhile Mercer suggested on Twitter that his question was meant to ask whether Khan felt he was receiving a “homecoming”.
The BBC said: “Our reporter asked the Mayor a question in the context of the trip being referred to by senior politicians in the region as a homecoming. The full answer the Mayor gave shows he understood the context of the question.”
This article has been updated.