Södersjukhuset already has the largest emergency care unit in the Nordic region and runs a round-the-clock walk-in clinic for women and girls who have been sexually assaulted in the city, treating between 600 and 700 patients a year.
On Wednesday, the hospital announced that from mid-October, it would also admit men and boys as part of a strategy to ensure "gender equal" emergency care for rape victims of both sexes.
In 2014, some 370 cases of sexual assault on men or boys were reported across Sweden, according to the Swedish National Council for Crime Prevention, although experts believe that the actual figure is much higher.
"The general perception is that men cannot be raped," Lotti Helström, a senior physician at the hospital told Sveriges Radio, adding that male victims can suffer even more than women.
"In studies, the health effects are shown to be greater for men, both in terms of physical health and mental health. There is a greater risk of a raped man getting post-traumatic stress disorder," she said, adding that the subject of male rape remained "extremely taboo".
Helström explained that men were much more likely to be raped by other men than by women and said that the experience could lead to "sexual identity" problems in the future.
Sweden has the highest rape rate in Europe, a statistic that gained global prominence in 2010, when Wikileaks founder Julian Assange was first accused of sex crimes
in the Nordic nation, allegations which he still strongly denies.
It is worth noting that the country records allegations in a different way to most other countries, tracking each case of sexual violence separately. So for example if someone says they were raped by a partner every day for a fortnight, officers will record 14 potential crimes. Elsewhere, many countries would log the claim as a single incident.
Nevertheless, the nation's high statistics have made rape a matter of high level political debate in recent years.
Last year, a study by gender equality organisation RFSU suggested that in most municipalities across Sweden, men were uncertain where they could get emergency help following a rape.
On Wednesday, Inger Björklund, a spokesperson for the group told The Local that it strongly welcomed the new facility.
"There are myths about masculinity that make it difficult for men who have been sexually traumatized to talk about their experiences," she said.
"A clinic focusing on men who have been sexually abused will contribute to the awareness of experiences of sexual abuse among men and make it more possible to meet men's needs."