'From the age of about eight I knew something wasn't right with me," says Benson, a 17-year-old from Cumbria. "But it was never an issue because I was just a kid having fun. When I hit puberty and started growing breasts, I looked at other boys and thought, No – that's the way I am supposed to be. I had no idea what transgender was. The internet helped a lot and I began to read blogs. I never came out to my family; they just guessed, really." At 16, he went to the doctor.

Benson Bell – or Ben to his friends – was born a girl. He is now hanging out on the set of Hollyoaks to swap tips with Victoria Atkin, the actor portraying a transgender boy as part of a controversial new storyline on the teen soap opera. He is one of a group of teenagers with gender identity disorder who have been working in secrecy with the show for the last few months. Also known as gender dysphoria, gender identity disorder is defined as feeling that you were born into the wrong gender. Up to 100 children a year – aged up to 18 – are referred to the specialist Gender Identity Development Service (Gids) at the Tavistock and Portman NHS Foundation Trust. Doctors estimate that of those who are referred pre-puberty, only around 20% will actually change gender. But of those who present post-puberty, up to 80% will go on to have hormone treatment and surgery, as Benson hopes to do.

Early next month, Hollyoaks will follow the character of Jasmine, a 15-year-old girl, on exactly this journey. Jasmine has always felt like a boy and dresses as one in secret. The storyline will chart her transition towards becoming "Jason", coming out to friends and family and taking hormone-blocking treatment.

Benson agreed to help out in the hope that the show will convey what it is really like to be a trans teen. Although Benson has not started the hormone treatment that could lead to gender reassignment, he is able to live as a boy and his friends have considered him as such for the last two years. But his family still sometimes refer to him as a girl. "I respect them for it, but they don't accept me at all," he says. "It's hard for my dad, especially. I was his little princess and all of a sudden this happens. He says he is never going to accept it and it's a phase. Hopefully, in time he will see that this is the way I'm meant to be and start seeing me as his son. But I can't guarantee that will happen and I have to do this with or without my parents."

This experience mirrors the Hollyoaks plot: Jasmine's parents are an ex-model and ex-footballer – and horrified that their blonde trophy daughter identifies as male.

Victoria Atkin, 23, is the actor playing Jasmine/Jason. It's her first television role, and she says she has drawn on Hilary Swank's performance as Brandon Teena in Boys Don't Cry, the real-life story of a 21-year-old transgender man who was raped and murdered in 1993 after male friends discovered he had female genitalia. "But," says Atkin quickly, "we are not dealing with it in such an extreme or violent way."

Swank prepared for the part by living as a man for a month. Her neighbours were so convinced, they thought her brother had moved in. Atkin will start strapping her chest regularly to play the role of Jason and is contemplating what to do with her long blond hair. At the moment she plays Jason in a beanie hat.

Atkin – whose last role was as Cinderella on tour – knew very little about the transgender world before meeting Benson and other transgender teenagers. "It was a big revelation for me how much taunting and bullying there is. The trauma and the effect on the family is huge. The impact on siblings at school, for example, came up with a lot of the people I have spoken to. They are often attacked, too."

Atkin is having to transform herself physically for the role. She says it is a relief when she can change out of "Jason's" jeans at the end of the day, though. "You sit differently in men's clothes."

To date, the youngest transgender character in a soap opera appeared in the US drama All My Children in 2006, which featured 19-year-old rock-star character Zarf/Zoe. Meanwhile, Coronation Street's Hayley Cropper (birth name "Harold" — played by Julie Hesmondhalgh) has been part of the cast since 1998 and is apparently still the only permanent transsexual character in any serial drama in the world. Hollyoaks' decision to portray a 15-year-old is controversial, but perhaps timely. In the last year, Gids has had 97 referrals, up from 50 in 2007. Fifty-four per cent are aged 15 or over, the rest are 14 or under.

There are marginally more boys referred than girls. "Girls can live as a tomboy for much longer when they're younger, so it often doesn't show up as a problem," explains Dr Victoria Holt, consultant child and adolescent psychiatrist at Gids. "We are getting more referrals all the time because people are more aware of the issue now. Some GPs will still say, 'It's just a phase.' But even if it is just a phase – and with some, it is – the young person should be listened to." She hopes Hollyoaks will put across the message that gender identity and sexuality are not the same thing. "People confuse them all the time. But they are fundamentally different."

Daniel (not his real name), an 18-year-old student also from the north-west of England, born a girl, agrees with this: "I'm a heterosexual male. I never doubted that. The simple fact is this: the body I have is not my body." He too has been working with the production team. He called himself by a boy's name from the moment he could talk and has always refused to wear girls' clothes. "All my life I have thought, Why do I have a female body? I have had a [female] partner for two years and I refuse to let her touch me because it's not my body." Daniel started taking hormone blockers earlier this year, to stop menstruation. From next year he will begin testosterone treatment and then progress to surgery. "One surgery for the chest [mastectomy], one for the uterus and one for your male phallus. I want the full haul. Because I'm a man, and the sooner I get there the better. I'd like to do it by the time I'm 24 so that I can start my life."

The process of complying with NHS regulations and undergoing constant supervision is lengthy and not one you would undergo lightly, he adds. "You can go abroad and get it all done quickly. But you're better getting it done here on the NHS than in a chop-shop abroad."

Hollyoaks' Jasmine/Jason has all this ahead. Series producer Paul Marquess, who has worked on Coronation Street and Footballers' Wives, is adamant that the transgender storyline is not about chasing ratings. "I don't think it's sensationalist. Yes, that's a pitfall but I think we've avoided it." He has his own reasons for trusting it will work. "I grew up gay in Belfast in the 1970s when there was no one to talk to, no positive role models, no gays on Corrie. I knew that absolute isolation of not knowing who to turn to. So it's not about ratings. It's about how people are affected by this." As teenagers we all know about keeping secrets, he adds. "Our audience will identify with having feelings that you can't express to your friends, teacher and parents. This is just a different way of looking at it."

But one parent of a transgender child who was born a boy but is now a woman (in her early 20s) tells me off the record that she is slightly horrified at the idea that this situation might be portrayed as emblematic of the problems of adolescence. "On television these things can be done fantastically well – like the Channel 4 documentary The Boy Who Was Born a Girl. But I'm very disappointed if they say they're equating it with a normal teenage experience. If that's the case, they have completely not got it. It's nothing at all like what most teenagers go through. The issues connected with being gay, for example, are not as life-shattering as being unhappy in your gender. On the one hand, I welcome anything that will be educational. But, believe me, this really is outside the realm of anyone's 'ordinary' experience."

Benson, however, has high hopes the show will raise awareness and stop bullying of trans teens. "People still shout abuse at me in the street," he says. "They call me a lesbian and I always think, You could at least call me a tranny. Get it right." Seeing someone like himself in a daytime soap makes him feel proud. "I hope they'll show the shyness of it. That you're always on edge, wondering if other people think you're a boy or a girl. It's very depressing as well, to be honest. But my hope is that this programme is so big, people will realise they can't hide from it any more and pretend it's not happening. I hope they realise it's not wrong and it's not something you put on or that you want to do. You're born with it."

• This article was amended on 2 July 2010. The original said that children from babies to 18-year-olds can be referred to Gids. This has been corrected.

Hollyoaks is on Channel 4 on weekdays at 6.30pm, with an omnibus edition on Sundays at 9.50am.