The HPV vaccine is being offered to men aged 16-26 who have sex with men from January onwards.
Schoolgirls currently get the vaccine in school, to guard against cervical cancers.
However, the vaccine also covers other cancers and genital warts.
Research shows that where there is a high take-up of the HPV vaccine among teenage girls, heterosexual boys and men also benefit from the so-called "herd immunity".
Clinical lead of the HSE’s Sexual Health Strategy, Fiona Lyons, says this has been clearly demonstrated in Australia.
"They first introduced the vaccine for adolescent girls in 2007, and they have had a significant decline, practically no genital warts being seen now in Australia within the heterosexual population," she said.
"But because it wasn't being given to at-risk groups, the men who have sex with men were not benefitting from that herd immunity.
"And it's with that in mind that we've introduced the HPV vaccine for men who have sex with men from next January."