The defence ministry would not confirm if the order was prompted by the North's artillery firing or South Korean drills in response.
However, a text message sent to residents and confirmed by an island official cited "naval fire" to be conducted by South Korean troops from 3 p.m.(0600 GMT) Friday.
An official on Yeonpyeong island, which sits just south of the disputed Northern Limit Line (NLL) sea border, said the evacuation was ordered for residents to move into shelters on the island at the request of the South Korean military.
The firing by North Korea caused no civilian or military damage in the South, South Korea's military said in a news briefing.
"This is an act of provocation that escalates tension and threatens peace on the Korean peninsula," a spokesman for the South Korean Joint Chiefs of Staff said.