The company, which runs services in Hastings, Bexhill, Rye and Eastbourne, becomes part of the Govia Thameslink Railway franchise in July and says the ban falls in line with GTR policy.
A spokesperson for Southern said: “From Sunday July 26, electronic cigarettes and other electronic ‘vaping’ devices will no longer be permitted on Southern and Gatwick Express trains and at Southern stations.
“On that date, Southern and Gatwick Express become part of the Govia Thameslink Railway (GTR) franchise.
“GTR already has this policy and we are changing ours to fall into line with the GTR policy.”
Although Southeastern, which runs train services between Hastings and London Charing Cross via Battle, currently has no such ban on e-cigarettes, the company said it is considering taking similar action.
A spokesperson for the company said: “While we have not got a ban at the moment, it’s something we are looking into.”
There is currently no law against using e-cigarettes in England. But people will be banned from using e-cigarettes in enclosed places such as restaurants and pubs in Wales, under a new public health law, which is likely to come into force in 2017.