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 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.
South Korea's military told the village there was firing at sea by the South Korean military after "a situation" near the border, the official said. But it was not clear whether it was a drill or had some other cause.
Residents of Baengnyeong island which lies far to the west of Yeonpyeong and also near the sea border, were also told to evacuate, a village official there said.
In 2010, North Korean artillery fired scores of rounds at Yeonpyeong island, killing four people, including two civilians, in one of the heaviest attacks on its neighbour since the Korean War ended in 1953.
North Korea said at the time it was provoked into the attack by South Korean live-fire drills that dropped shells into its territorial waters.
