The television network says it has no plans to air the episode again soon.
Fox spokeswoman Gaude Paez said Family Guy Boston Marathon episode had been removed from Fox.com.
In the episode, main character Peter Griffin has a flashback about crashing into runners with his car and making friends with a terrorist plotting to blow up a bridge.
When Peter, who is voiced by Seth MacFarlane, dials a mobile phone a friend has given him, explosions and screams are heard in the background.
The episode was originally aired on March 17 in the US.
On some websites in America, an edited clip has been circulating that mixes the two scenes together, making it seem as though the explosion was at the marathon.
Some commenters have since implied that the show “predicted” the bombings.
Family Guy creator Seth MacFarlane criticised the edited clip on Twitter and offered his condolences to the victims of Monday’s bombings at the Boston Marathon.
Seth said: “The edited Family Guy clip currently circulating is abhorrent. The event was a crime and a tragedy and my thoughts are with the victims.”
Meanwhile, Film4 has taken the film Four Lions out of its schedule next week after the Boston Marathon bombings.
Chris Morris’s comedy is about a group of British Muslims planning a bomb attack at the London Marathon.
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