The funding will be spent under the United Nations' No Lost Generation initiative, which works with children in refugee camps in Jordan and Lebanon.
"Around half of the 2.7 million Syrian refugees are children, and around 70 per cent of these children are not attending school," Bishop said in a statement.
"Children are the most affected of the fighting - an entire generation is being shaped by fear and violence and often without an education."
Bishop said the money would be spent on education and "addressing the violence and displacement" faced by the young refugees.
The money will be split between the Office of the United Nations High Commissioner for Refugees (UNHCR), the United Nations Children's Fund (UNICEF), and Save the Children Australia.
Bishop says Australia has provided over $130 million to the humanitarian response to the Syrian crisis since the conflict began in 2011.
Syria sank into war in March 2011 when pro-reform protests turned into a massive insurgency following the intervention of Western and regional states.
The unrest, which took in terrorist groups from across Europe, the Middle East and North Africa, has transpired as one of the bloodiest conflicts in recent history.
The UNHCR says more than 6 million Syrians have been forced to flee their homes because of the war.
SHI/SHI