Several hundred viewers also complained to the BBC after the scene where Queen Vic landlady Linda Carter was raped.
Her character, played by Kellie Bright, was attacked by Dean Wicks (Matt Di Angelo) in the episode which went out on BBC One at 8pm.
An Ofcom spokesman said: “Ofcom is currently investigating a rape scene broadcast in EastEnders on October 6 which received over 90 viewer complaints.
“We are investigating whether the programme was appropriately scheduled and if it met generally accepted standards.”
A peak audience of 7.3 million tuned in to the episode and the BBC defended it after the broadcast, citing the soap’s ‘rich history’ of showing difficult storylines.
In a statement, it said: “EastEnders has a rich history of tackling difficult issues and Linda’s story is one of these.
“We have worked closely with Rape Crisis and other experts in the field to tell this story which we hope will raise awareness of sexual assaults and the issues surrounding them.
“We have been extremely mindful of the content within the episode and the timeslot in which it was shown and at no point have there been any scenes of a graphic nature. In fact, the attack on Linda was implied and was not explicit.”