It will provide extra antenatal support with specially-trained midwives, psychologists and paediatricians.
Co-run by Barts Health NHS Trust in London, the scheme could be introduced in other UK hospitals if successful.
Consultant midwife Inderjeet Kaur said the extra care was "so important" as giving birth could trigger frightening, graphic memories of an attack.
One in five women between the ages of 16-59 in England and Wales has experienced some form of sexual violence, according to official statistics.
BBC News spoke to three rape victims about their experiences during childbirth - two of them helped design how the clinic would operate.
Melanie (name changed for confidentiality), aged 37, had her baby two years ago.
She said: "I was given gas and air whilst in labour and I started hallucinating, seeing the man who had attacked me in the room. I managed to articulate what was happening to my husband, but he didn't know what to do.
"He wasn't equipped to deal with it at all, and there was no-one else in the room who was either. I was terrified and screaming. Nobody asked me; I wish I'd had some control."
'I cried and cried hysterically': Three women describe their traumatic experiences
Though the service will be integrated into a regular maternity ward at the Royal London Hospital, women will follow a different antenatal route from the moment they are referred.
As well as being offered extra, longer meetings with specially-trained staff, women will be able to have more of a say as to how their birthing rooms are laid out and legal advice over their medical checks.
The clinic will also provide antenatal classes and breastfeeding advice which has been altered for women who have experienced sexual attacks, and offer specialist gynaecological examinations and mental health support after labour.
It also plans to offer women in other countries one-off appointments in the form of video calls.
Pavan Amara, founder of the My Body Back project which jointly established the clinic with the Barts Health NHS Trust, has met a number of women who told her of traumatic experiences during their pregnancies.
She said: "One woman was told by her rapist: 'If you relax it'll be over with quicker.'
When the woman was told the same thing in a healthcare setting, "the health professional was completely unwittingly and unknowingly echoing the words of the rapist".
"It had a huge impact on the woman mentally. It's things like this... very small, but very big for a woman who is vulnerable."
Women can self-refer to the maternity clinic by emailing the team to make an appointment.
Ms Amara explained: "They don't have to say what happened, although they can if they want to. Whatever they feel is right for them. We will then book them an appointment and take it from there."
She said support for women in other countries would be conducted out-of-hours in the team's own spare time.
The team had received many international emails from women who cannot use NHS services, she said, adding: "We don't want to leave them with no option, we want to do something for them."
Ms Amara, who was raped as a teenager, waived her anonymity as a victim when she helped set up a sexual health clinic at the hospital for victims of sexual violence last August. With more than 800 women using the service since it was set up, talks are under way to open a similar unit in Glasgow.
One rape victim explained how her body "went into complete shock" when she went into labour.
"I just couldn't open my legs for the baby to come out," she said.
"There was an emergency so they took me straight down to the operating theatre. It was very noisy and it was very busy.
"There were bright lights and just lots and lots of people around. And, I think for me, because there had been lots of people there in my rape and lots of people watching what was going on, it just brought back so many memories.
"It was very traumatising."
The victim, who wished to remain anonymous, believes the new clinic will help others.
"Just by virtue of walking through the door, people know something of what's happened to you. So you've said it without saying it which is often the hardest thing," she said.
Consultant midwife at the clinic Inderjeet Kaur said often women did not want to talk about what had happened to them.
This could mean medical staff are unhelpful without even realising it, for example by using the wrong language.
"This is so important because these women are so vulnerable - we shouldn't be contributing to their trauma," she said.
The UK's first maternity clinic for women who have been victims of rape and sexual assault has opened.