The senior Samajwadi Party (SP) leader said that he was subjected to insult and humiliation for about 10 minutes because he was a muslim.
Even Shahrukh cited the same reason that because of his religion, US authority insulted him in the airport during two of his visits to the country.
The senior SP leader travelled to US to take part in an event at Harvard University.
Khan, who is accompanying Uttar Pradesh Chief Minister Akhilesh Yadav for the presentation of a Harvard study on the Kumbh Mela pilgrimage, was detained for about 10 minutes for "further questioning" at Boston Logan International Airport, informed Indian officials.
India has lodged a formal complaint with US against the treatment meted out to SP leader.
In Washington, Indian embassy spokesman M Sridharan said the mission has "taken up the issue with the State Department officially and we have conveyed our serious concern."
"We have asked them to intervene and take appropriate measures to avoid recurrence in the future."
Khan, the press release stated, said that he had gone to America not for a pleasure trip but on the invitation of Harvard University to deliver lecture on how the state government organised Mahakumbh mela in Allahabad earlier this year.
The Mahakumbh is the largest religion congregation lasting for three months. It saw participation of over 10 crore people from across the world.