Margaret MacDonald spoke out about Tabeetha School in Jaffa to mark UN International Day of Peace on Thursday.
The Church of Scotland institution has a mix of 339 Christian, Jewish and Muslim children from across the world.
Ms MacDonald, of Bo'ness in West Lothian, said: "The school is a special place and the Church of Scotland's presence in this country is very important.
"It is a bright light in a very difficult land.
"It is a land of fear where there is mistrust and lack of understanding among the Jewish and Arab communities.
"The Church of Scotland brings both groups together."
She added government-run schools in Israel generally cater to individual communities, which leaves little opportunity to learn about anyone different from themselves.
Tabeetha, founded in 1863, is one of the few places in Israel where children and young people of different languages, faiths, cultures and histories are educated together in English.
It has 34 teachers from around the world and has formed a new twinning partnership with Braes High School in Polmont, near Falkirk.
To mark UN International Day of Peace, which commemorates the ideals of peace, a joint no-uniform day is being held at both schools.
Pupils at Tabeetha will wear white, green or yellow and youngsters at Braes will sport blue, red, green and yellow - the schools' house colours.
Ms MacDonald said: "We pride ourselves in developing an intellectual, spiritual and social awareness in all our pupils, regardless of race, ability, gender or religion.
"There are children from all over the world rubbing shoulders every day and at the moment there are some 40 different languages and dialects spoken.
"Arabs learn about Jews and vice-versa which gives them confidence to go out into the world of work, able and willing to work with people of all religions and none."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.
