Protecting Children's Health in Schools Act of 2006 - Amends title XIX (Medicaid) and XXI (State Children's Health Insurance) (SCHIP) of the Social Security Act (SSA) to establish requirements for providing and receiving reimbursement for school-based health care for children, including children with special needs, and the related administrative and transportation costs covered under Medicaid. Includes health care provided through Medicaid managed care organizations.
Directs the Secretary of Health and Human Services and the Secretary of Education, acting jointly, to develop and implement a uniform methodology for claims under this Act.