The plant supplies most of Lithuania's electric power.
Lithuania has shut down its one and only nuclear power station in Visaginas.
The Ignalina plant, the only nuclear reactor in the Baltic states, stopped producing electricity at 2300 local time (2100 GMT).
The closure of the Soviet-era plant was a condition of Lithuania's membership of the European Union.
The move will mean an increase in power prices for Lithuanians and more reliance on Russia for energy supplies.
Just before the shutdown, Energy Minister Arvydas Sekmoka said: "We are keeping our word to our European partners."
The facility was opened 26 years ago, when Lithuania was still part of the former Soviet Union.
It was built to the same design as Chernobyl, which was behind the worst civil nuclear disaster in history when one of its reactors overheated in 1986.
BBC correspondent Gabriel Gatehouse says Brussels insisted the place be closed down, and allocated around 820m euro (£731m) to cover part of the costs of decommissioning the plant.
But critics said that Ignalina still has another 10 to 15 years of life in it and that the risks of an accident are minute.
Aleksei Tichomirov, a resident of Visaginas and an engineer at the plant, said he was unable to understand why the energy source had to close.
"Why throw away a good thing that could still serve for years", he said.
The plant supplied up to 80% of Lithuania's electric power.
Our correspondent says the shut-down will mean higher electricity bills at a time when the country's economy is shrinking rapidly.
It will also mean that, fewer than 20 years after the collapse of the Soviet Union, Lithuania will once again become dependent on Moscow for much of its energy supply.