Sailors' Society has provided two motorised boats which carry up to 30 school children each.
It is for the journey from five islets to the mainland Sulangan Integrated School.
The Christian charity raised money for the boats as part of its mission to help seafarers and their families around the world.
Before the boats were introduced, the children had to wade through the sea to reach the school, which is around a mile and a half away.
Ramie Aronales, 16, who has disabilities including breathing difficulties and his siblings Rose Marie, 12, Marvin, 8 and Marvy, 6, used to swim from their home on the tiny islet of Biagayag each day.
Their father would carry the youngest child, Marvy on his back at low tide, and at high tide the children were sometimes unable to get to school at all or would be trapped at school until it passed.
Their parents did not get the opportunity to finish their education, but the children hope to do so.
16-year-old Ramie said: "The school boat project brings us, and other families like us, so much joy because at last we won't be late and won't miss going to school ever again.
"This will serve as a stepping stone for me to become a seafarer someday."
Sandra Welch, deputy CEO and director of programme for Sailors' Society, said: "The worst thing most of us face on the school run is a bit of traffic, so it's hard to believe that there are children who have to swim through the sea just to get an education.
"Thanks to these boats, the children of Sulangan Integrated School no longer face an exhausting, dangerous journey every morning and arrive at school safe, dry and ready to gain the schooling they need."