The funding is part of an $80 million pot distributed to 197 centers around the nation.
Much of New York's share is coming upstate, including the North Country Children's Clinic in Watertown, NY.
The capital is earmarked for construction and renovation, and aims to allow school-based health centers - physician-run clinics that work in conjunction with school nurses, staff, and parents - to serve more students and expand access.
The largest portion of New York's funding; over $1 million, will go to three providers in Rochester, with operations in Schenectady, Albany and Watertown receiving lesser amounts in that order.
Spokesperson for the health resources and services administration, Martin Kramer says the funding was made possible by the affordable care act, and is crucial for the development of such clinics.
"School-based health centers provide a combination of primary care, mental health care, substance abuse counseling, dental health, nutrition, education, and promote healthy activities. So it's incredibly important that these school based health centers receive funding, so they can continue that work."
Kramer says the funding was awarded based on the quality of applications.
New York State overall received 17 separate awards, the second highest number of awards for a state nationwide.
Reporting by the Innovation Trail is supported by the Corporation for Public Broadcasting. Visit innovationtrail.org.