Kenyan boys will wait longer before they can also receive the human papillomavirus vaccine that prevents some cancers.
At least 800,000 girls aged 10 years will receive two doses of the vaccine beginning this month to prevent cervical cancer.
Public health officials said it was more effective to target girls because 99 per cent of cancers caused by HPV affect women.
Recently, some countries like Britain and Australia began vaccinating boys because HPV also causes penile and anal cancer in men, as well as genital warts.
Head of the Vaccines and Immunisation Programme Dr Collins Tabu said in future the government might consider boys, once all girls have benefited.
"Remember we are introducing the vaccine to protect our girls from cervical cancer. We do know that the vaccine might be able to protect against other conditions such as genital warts, anal cancer and even oesophagal cancer," he said.
Like any virus, there is no cure for HPV, but it is preventable through vaccination.
Studies show that because HPV is mostly sexually transmitted, vaccinating boys and men also helps protect women.
"While it might be looked at from that perspective, we may need to consider that it is probably most cost-effective to target the girls and by extension, if the girls are disease-free we then have the benefits extended to the boys as well," Tabu told the Star.
Benda Kithaka, co-founder Women 4 Cancer NGO said although some countries vaccinate boys, it was cost-effective for Kenya to begin with girls.
"Boys may be affected by penile or anal cancer but 99 per cent of cancers caused by HPV affect the cervix so for public health approach and to ensure safety, we are offering women and girls," she said.
"If parents choose to vaccinate boys they can go to a hospital and they will be vaccinated at a cost," she added.
The two spoke when the Ministry of Health announced that more than 800,000 10-year-old girls will receive two free doses of the HPV Virus vaccine beginning this month.
The exact date has however not been communicated. The vaccine will be introduced into the routine immunisation schedule.
The roll-out was to be done since early last year but has been postponed several times.
“It was not by design that we had to keep shifting. One of the considerations before you start introducing a vaccine as a country and as a rule into the immunisation schedule, you must be assured of the continuous uninterrupted availability of that particular vaccine across all levels,” Tabu said.
He added, “Once you start vaccinating against a disease, you do not stop unless one of two things happens: you have eradicated the disease against which you are vaccinating or Jesus comes whichever happens first.”
Once introduced, a caregiver to any 10-year-old girl will be able to walk into any healthcare facility and access the HPV vaccine free of charge.
(edited by O. Owino)