The American Academy of Pediatrics recommends periodic oral health risk assessments (OHRAs) for young children to prevent early childhood caries and promote oral health. The objective of this quality improvement project was to incorporate OHRAs, including documentation of the oral screening examination, into well-child visits for patients aged 12 to 47 months to drive (1) improved rates of preventive fluoride varnish (FV) application and (2) improved dental referrals for children at high risk for caries. We identified a quality gap in our OHRAs, oral examination completion, FV application rates, and dental referral rates via retrospective data collection. Plan-Do-Study-Act cycles targeted modification of electronic medical record templates, oral health education, and standardization of work processes. Process and outcome measures were analyzed with statistical process control charts. At baseline, OHRAs and oral screening examinations were documented in <2% of patients. Of eligible children, 42% had FV applied. Routine dental referrals before age 3 years were uncommon. After multiple Plan-Do-Study-Act cycles, documentation of OHRAs and oral screening examinations (process measures) improved to 45% and 73%, respectively. The primary outcome measure, FV rates, improved to 86%. Referral of high-risk patients to a dentist improved to 54%. A systematic, evidence-based approach to improving oral health, including electronic medical record-based interventions, resulted in improved documentation of oral health risks and oral screening, improved rates of FV application in young children, and increased identification and referral of high-risk patients.