It comes after protests took place in the village of 700 people against the holiday homes that are taking over the area.
Cllr Cemlyn Williams, Gwynedd Council, said: “It is always sad when the future of a school is under consideration.
“However, we have a duty to ensure that we provide the best possible education and experiences as well as the best possible learning environment.
“After fully considering all objections, it is recommended to confirm the proposal to close Ysgol Abersoch at the end of 2021.”
About 39 percent of the houses in the village are second homes.
“It’s not fair to the locals,” said Councilor John Brynmor Hughes.
“We are the people who sold our hearts out of our communities in the first place, and the land for developments.”
Demand for second homes and vacation properties has exploded due to the combination of Brexit and the coronavirus pandemic.
Impact of Brexit
Brexit would have made life in a second home abroad more difficult, while rural areas have attracted people living in cities with the increase in working from home.
Mabon ap Gwynfor, Senedd’s Welsh member for the Abersoch region, said: “This has been an ongoing problem for at least two generations.
“It has come back to the fore in the last 12 months or so, mainly because of the coronavirus. But it was clearly a problem before that.
“In 2019, I saw this as one of the major issues facing the community, as at the time, around 30% of the high-end homes sold in Gwynedd were being sold as second homes.
“It’s damaging because it takes a house out of the building stock. It increases the value of houses, so only the wealthiest can afford it.”