The company's vaccine Gardasil protects against four strains of the human papilloma virus, which can cause cervical and anal cancer, and genital warts.
In 2007, the National Advisory Committee on Immunization recommended that girls and women aged nine to 26 be vaccinated for HPV. In 2012, NACI included males of the same age in that recommendation.
P.E.I. was among the first provinces to introduce school-based HPV vaccination programs to girls.
"P.E.I.'s decision to include boys is an important milestone in protecting both males and females against the diseases that can result from HPV infection, such as genital warts and anal-genital cancers," Dr. Mauricio Ede, medical director at Merck Canada, said in a release.
"Both males and females contribute to the spread of HPV and both develop diseases as a result of HPV infection."