Supporters of the Core Issues Trust, which promotes the idea of a cure for homosexuality, distributed the pamphlet asking "Is Boris Lying?" in the constituency he was standing for.
Core Issues placed its ad in response to one from campaign group, Stonewall, which stated 'Some people are gay. Get over it!'.
The Charity's advert, which read 'Not gay! Ex-gay, post-gay and proud. Get over it!", was banned, hours before it was due to appear on London buses.
Core Issues Trust lost the case and in the leaflet claims it's now being pursued for a £100,000 legal bill.
The leaflet states: "Don't vote for Boris if you respect diversity, equality and justice for all".
The Electoral Commission states that "is an illegal practice to make or publish a false statement of fact about the personal character or conduct of a candidate in order to affect the return of a candidate at an election".
Mike Davidson, director and founder of Core Issues Trust said: "The voters in Uxbridge and South Ruislip need to know the depths to which Boris Johnson is prepared to sink for political advantage and to cover his tracks..
"Is this really the kind of person they want to represent them in parliament?"
BTP Duty Officer Anthony Capon told BuzzFeed: "We are aware of an issue relating to the distribution of politically motivated leaflets on rail services on the Metropolitan line during the course of Thursday, 7 May.
"We thank those who have brought the issue to our attention and will now seek to investigate the matter in the most appropriate manner."