Teachers will also be stopped from buying coffee products at work as part of a wider government campaign to reduce the consumption of food and drink high in caffeine and calories.
High-caffeine products such as energy drinks were already restricted in South Korean schools, but coffee was typically available in vending machines and kiosks for teachers.
The ban, which comes into force on 14 September, will mean coffee cannot be sold in any primary or secondary school across the country.
"The revision aims to create healthy eating habits among children and teenagers," a Ministry of Food and Drug Safety official told the Korea Times. "We will make sure coffee is banned at schools without fail."
The ministry said there were concerns about coffee causing dizziness, heart palpitations, sleep disorders and anxiety among pupils, many of whom reportedly turn to high-caffeine products to stay alert during lessons.
"We have notified schools of the coffee ban across the nation through cooperation with the education ministry," the official said.
South Korea’s coffee consumption has doubled since 1990 in a boom stimulated by the arrival of Starbucks.
In 2016 the country consumed 2.3kg of coffee per person, according to the International Coffee Organisation. The figure is one of the highest among Asian countries, although only roughly half the amount consumed by the average American.
The number of coffee shops in South Korea more than tripled between 2011 and 2015, from 12,400 to 49,600.
South Korean health officials has previously prohibited adverts for unhealthy food and drinks from being shown during the times children are most likely to be watching TV.
The school coffee ban comes as the British government launches a consultation on plans to stop shops selling high-caffeine drinks to young people.
The scheme could see retailers banned from selling energy drinks to under-16s and possibly even under-18s.
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