Khan, 68, arrived here on Thursday, and was given a guard of honour at the airport.
Despite being in the city, Vijayan failed to greet the new Governor at the airport, but made it up by calling on Khan at his residence later in the day.
Khan replaces P.Sathasivam, a former Chief Justice of India, who demitted office after the end of his five-year term and returned to his home town Erode in Tamil Nadu.
Hailing from Uttar Pradesh, Khan entered politics as a student leader at the age of 26. He has been a member of the Uttar Pradesh Legislative Assembly and as well as the Lok Sabha and served as a Union minister in the Cabinets of former prime ministers Rajiv Gandhi and V.P.Singh.
In his long political career, Khan has changed several parties -- starting from former prime minister Charan Singh's Bharatiya Kranti Dal, Congress, Janata Dal and Bahujan Samaj Party. In 2004, he joined the BJP, but quit three years later.
His progressive Muslim stand and strong opposition to Triple Talaq is what helped open the Kerala Raj Bhawan doors for him.
The BJP, which is trying hard to make a space for itself in Kerala's electoral politics, has played the political card by posting Khan in the state, which has a significant Muslim population. Khan, who is known to keep a low profile and is expected to be a no-frills Governor.