School-Based Health Clinic Establishment Act of 2009

School-Based Health Clinic Establishment Act of 2009 - Amends the Public Health Service Act to require the Secretary of Health and Human Services (HHS) to award grants for the cost of operating school-based health clinics (SBHCs) to provide comprehensive primary health services during school hours to children and adolescents by health professionals.

Requires SBHCs to: (1) provide services to children and adolescents for whom parental or guardian consent has been obtained; (2) provide on-site access during the academic day when school is in session and have an established network of support and access to services with backup health providers when the school or SBHC is closed; and (3) comply with federal, state, and local laws concerning patient privacy and student records.

Allows the Secretary to: (1) give preference to applicants who demonstrate an ability to serve populations of children and adolescents that have historically demonstrated difficulty in accessing health and mental health services; and (2) waive certain requirements under this Act for no more than two years.

Requires the Secretary to establish a program to provide technical and other assistance to SBHCs.