Displays of tobacco products in the stores will be allowed only temporarily in "certain limited circumstances," The Daily Telegraph reported.
Smaller stores and news agents will have until April 2015 to comply with the ban.
"We cannot ignore the fact that young people are recruited into smoking by colorful, eye-catching cigarette displays," Health Minister Anne Milton said. "Most adult smokers started smoking as teenagers, and we need to stop this trend.
"Banning displays of cigarettes and tobacco will help young people resist the pressure to start smoking and help the thousands of adults in England who are currently trying to quit."
The tobacco industry has criticized the ban, saying it would encourage tobacco smuggling, increase the burden on shopkeepers and violate European Commission competition standards.
But the industry dropped plans to file a legal challenge against the ban.
The proportion of smokers in Britain has fallen from 45 percent of the population in 1974 to 21 percent today.