Pakistani media reported on Monday that she will be replaced by Munir Akram, who had done a stint as the permanent representative.
Akram was involved in an alleged domestic violence incident in 2002 just as Pakistan was taking its place on Security Council as an elected member and the US asked his country to lift his diplomatic immunity so he could be prosecuted.
But he managed to stay on till 2008.
Despite Maleeha Lodhi's campaign at the UN and Khan's intense diplomatic activity, only three countries, China, Malaysia and Turkey, joined Pakistan in raising the Kashmir issue - which meant they did not have any influence on the other 189 countries in the 193-member UN.
Khan acknowledged the failure, saying when he returned home, "Whether the world stands with Kashmiris or not, Pakistan is standing by them."
Lodhi survived a major snafu in 2017 when she held up a picture of an injured Palestinian girl in the General Assembly claiming that she was a Kashmiri and the hoax was exposed.
She tweeted after Monday's announcement of her removal, "I had planned to move on after UNGA following a successful visit by the PM."
Lodhi has previously served twice as ambassador to the US, the second time covering the crucial period of the 9/11 al-Qaeda attacks on the US and the US-led action in Afghanistan in which Pakistan became involved as a logistics provider.
A former journalist, she has also been Pakistan's High Commissioner in Britain.
About Akram's appointment, Pakistan Today wrote, "Akram is a veteran diplomat and is one of the ambassadors who believe in hardcore approach towards India instead of appeasement."
He was Permanent Representative from 2002 to 2008 and has been the foreign secretary.
In 2002, a woman called New York police to an apartment complaining that she was being assaulted.
Police, who responded to the complaint, said the 35-year-old woman, Marijana Mihic, who described herself as Akram's "girlfriend," had bruises to her head and abrasions to her knees.
She told them that Akram had bashed her head against a wall.
Police said they could not arrest him because he had diplomatic immunity. The Manhattan prosecutor's office said at that time that it would prosecute him if his diplomatic immunity was lifted.
The mayor's office requested the State Department to get his immunity waives so that he could be prosecuted.
The US did not press its request to Islamabad to waive his immunity.
Pakistan was a member of the Security Council and the US was preparing to invade Iraq at that time.
He told the New York Post, "My government sent me here to represent my country. I came to stay - and my government wants me to stay."
(Arul Louis can be contacted at arul.l@.in)
( With inputs from IANS )