The joke, which was in season four of the animated comedy show, showed baby Stewie running naked through a shopping centre shouting 'Help! I've escaped from Kevin Spacey's basement!'
The clip has now resurfaced in the wake of Rapp's accusations that Spacey made sexual advances toward him in 1986, when he was just 14.
It is not the first time Seth MacFarlane, the creator of the series, has made a swipe at Hollywood sexual abuse accusations through sneaky humour.
The actor and director made a joke about Harvey Weinstein - who has been accused of sexual abuse and harassment by multiple high-profile stars - while announcing the 2013 Oscar nominees.
MacFarlane and Emma Stone had just finished announcing the nominees in the Best Supporting Actress category when MacFarlane said, 'Congratulations, you five ladies no longer have to pretend to be attracted to Harvey Weinstein.'
The new allegations against Spacey were made by Rapp, who is openly gay, in a story that was published by BuzzFeed on Sunday.
The actor is accused of 'laying down on top' of Rapp at a 1986 party when the Star Trek actor was 14 and said, 'He picked me up like a groom picks up the bride over the threshold. I was aware that he was trying to get with me sexually.'
Hours later Spacey issued a statement via his Twitter account.
Now, several Hollywood elite and fans of the actor, have condemned Spacey's justification of making sexual advances against a young boy.
Spacey, claims the accusations are a result of a 'drunken mistake' and the story, which he 'doesn't remember', has encouraged him to choose to 'live as a gay man.'