Government health advisers recommended use of the Bexsero vaccine last year, and the government has spent months negotiating over the cost.
The drug was owned by Novartis, which recently sold most of its vaccines business to GlaxoSmithKline.
Health Secretary Jeremy Hunt said Sunday he was "very proud that we will be the first country in the world to have a nationwide Men B vaccination program."
Babies will receive the vaccine at two months, followed by two further doses.
Meningitis is a bacterial infection of the lining surrounding the brain and spinal cord that most commonly affects children and teenagers.