After earning her medical degree and completing a residency in adult psychiatry and a fellowship in child and adolescent psychiatry at Albany Medical Center, Dr. Balkoski began her career at the hospital in 1993, later becoming chair of the Department of Psychiatry. Dr. Balkoski is credited with growing the size of the Psychiatry department several times over, tripling the number of patients served in the outpatient psychiatry clinic, and successfully reshaping the delivery of mental health services within the practice, the hospital, and the emergency department. She developed the evidence-based substance use intervention tool known as SBIRT (Screening Brief Intervention and Referral to Treatment) within Albany Medical Center's training programs, and mentored hundreds of residents, faculty, and advanced students in psychiatry and psychology. Her colleagues credit her for being a compassionate, caring, and skilled listener, always taking the time to make everyone feel supported and understood.

She retired from her role as Chair of the Department of Psychiatry in March 2022.