More than 1.1 million refugees have fled to the country, the largest group compared to a country’s population in the world.
More than 70 per cent are living below the poverty line, hungry and living in poor conditions.
The new scheme will begin soon, feeding 1,000 children at school in Antelias, on the outskirts of Beirut.
The project will be run by volunteers, including Lebanese and Syrian mothers, and will run up to six months at first, said founder Magnus MacFarlane-Barrow.
Last year, Mary’s Meals passed the milestone of feeding a million children a day in the poorest places in the world.
Lebanon is the 13th country Mary’s Meals works in, with other operations in Malawi, Liberia, Zambia, Kenya, Haiti, India and South Sudan.
The news of the pilot scheme was announced at the founder’s paperback book launch, held at Ealing Abbey, where Mr MacFarlane-Barrow gave a talk in the Virtus Lectures series.
His book, The Shed That Fed a Million Children, tells the story of how the charity began and the work it does across the world, earning Mr MacFarlane-Barrow a place on Time’s 100 most dangerous men in the world list.
Mr MacFarlane Barrow, speaking at Ealing Abbey, said: “It was very much a case of starting small and then people understanding our vision.
“The situation in lebanon and the plight of the refugees is something we all feel compassion for. We’ve been investigating how Mary’s Meals can help, and work with partners in the country and we’re glad we can.
“It’s the children that suffer. They’re torn from school and their homes.
“We’ll be helping a small number of children for now, but I’m glad we can help in some way.”
The United Nations said that two million children in Syria are in danger of becoming a “lost generation” – with evidence the longer they are out of school, the harder it is to get them back.
The next Virtus Talk is by Dr Ruth Valerio on May 18.
The series runs until July and will end with Ann Widdecombe on July 13.