The export deal is though to be Israel's largest ever and almost 18,000 tonnes are going to be sent to the war torn nation.
The export plan was initially discussed last year, but was put on hold due to conflict in Syria. The Israeli government is responsible for re-instigating it now.
The fruit's transportation will be overseen by the Red Cross and the UN.
Kenyan drivers have been hired to transport the apples, which are grown in the Golan Heights.
The region produces around 50,000 tonnes of apples per year, roughly one third of the national yield. Israel previously exported apples to Syria between 2005 and 2011.
