Health Minister Fred Horne says about 47,500 boys in Grades 5 and 9 are to receive the HPV vaccine next fall.
"Expanding the HPV immunization program will mean both boys and girls will be protected from HPV-related cancers," Horne said Thursday.
"Our investments today will reduce health-care costs tomorrow and, most importantly, prevent future cases of cancer in Alberta."
The vaccine protects against human papillomaviruses, which cause cervical cancer, head and neck cancers, anal and penile cancers and genital warts.
Alberta is the second province to include boys in HPV vaccine programs after Prince Edward Island.
The vaccination was first offered to Grade 5 girls in Alberta in 2008. Since then, the province estimates about 61 per cent of girls between the ages of nine and 13 have received the shots.
The program is voluntary and parents must consent to their child receiving a shot.
The Society of Obstetricians and Gynecologists of Canada has been urging provincial health ministers to include boys in HPV vaccine programs.
Society CEO Dr. Jennifer Blake said Alberta's decision to include boys in its program is "huge" because it will draw the attention of other provinces that are considering such a move.
Blake said it will also help reduce the stigma of the vaccine, which some groups and people have shunned because of its link to sexual activity.
"Right now it is being seen as something to do with girls and something to do with sex. Once it becomes just a vaccine that everyone gets it reduces that sexual connotation," Blake said from Washington.
"It is just something that you do. It is actually a phenomenal advance to reduce the risk of these cancers."
Blake said the vaccine will increase the rate of decline of HPV-related cancers. She said this is already happening in Australia, where the vaccine has been shown to be quickly effective.
Last year, the National Advisory Committee on Immunization, which reviews scientific literature on vaccines, supported vaccinating boys in a submission to the Public Health Agency of Canada.
Alberta was one of the last provinces to approve the HPV vaccine for girls. The move was opposed by some Catholic school boards on moral grounds.
Last November, the Calgary Catholic School Board reconsidered its opposition and voted to allow school-based HPV vaccinations for girls.
Horne said there is no indication that any school boards oppose extending the vaccine to boys.
The cost of the expanded program is expected to be $11 million a year.
Dr. James Talbot, Alberta's chief medical health officer, said recent research has shown almost all head and neck cancers in men under 40 are HPV-related.
"Vaccinating boys against HPV is critical to protecting the health and wellness of Albertans."