Mr Khan's address to a Fabian Society conference in London was interrupted by activists moments after he was introduced to the stage.
During the nonviolent protest, one member announced, "Ladies and gentlemen, we're here today to make a non-violent, peaceful citizen's arrest". That didn't pan out.
The Mayor sat down and flicked through a newspaper while police escorted the demonstrators away.
And in a dig at the USA president after Mr Trump described himself as a "very stable genius", Mr Khan said: "It is a pleasure to be here even though we were distracted by the actions of what some would call very stable geniuses".
Mayor of London Sadiq Khan during the opening ceremony of the World Athletic Championships.
A demonstrator holds a pro-Brexit sign and a U.S flag, at the speech by the Mayor of London Sadiq Khan.
But a protester, unperturbed by the reception, said: "We stand under Common Law jurisdiction".
The protest was seen to be in response to comments made by Khan following Trump's decision to cancel his visit to London next month because he was opposed to the location and price tag of the new United States embassy, which he was set to attend the opening of.
Security forces tried to eject the disrupters however they refused and said, "if you touch us, you'll be done for common assault".
"We're not leaving, we've paid for a ticket".
Trump called himself "a very stable genius" last week after accusations he was "intellectually incapable" of holding office.
He also accused The Fabian Society, where Mr Khan was about to speak, of "subverting" the constitution.
Trump said he abandoned his plans to visit the United Kingdom as he is "not a big fan of the Obama Administration" selling off the previous embassy and building a new one in an "off-location".