The clinical department of Harmony Hill School is comprised of Master Level Clinicians, Psychologists and an Art Therapist. Upon admission, each student is assigned a primary clinician whose responsibilities include psychotherapy; case management, crisis intervention services and ongoing consultation with education, medical and youth care staff.

Clinicians provide individual and group therapy to the youth, plus family counseling and time-limited individual adult and marital therapies. The Clinical Department has approximately six therapy groups in progress on at any one time. Two court mandated sexually aggressive youth treatment groups are maintained year round. Other groups, lasting 12-16 sessions, may address topics for: victims of sexual abuse, victims who have shown sexually aggressive behavior, children of substance abusing parents, adolescents who are experimenting with alcohol and/or other drugs, youth who have experienced significant losses, youth with very low self-esteem, anger management, and Art Therapy. Trying to stay attuned to the changing needs of its clients by offering new groups or by repeating groups for new clients is a major goal of the clinical team.

Clinicians act as liaisons to child welfare agencies. They also assist parents in connecting with community resources and in planning visitation. Visiting Resource homes are available for those children without families.