The aim of this study was to assess the knowledge, attitude, and practice regarding early childhood caries (ECC) prevention and implementation of medical setting-based caries prevention among pediatricians and dentists in Taiwan. Data were collected from currently practicing pediatricians and general and pediatric dentists using self-administered questionnaires. A total of 301 questionnaires were completed by the pediatricians (n = 105), general dentists (n = 117), and pediatric dentists (n = 79). The pediatric dentists obtained significantly higher knowledge and practice scores than the general dentists and pediatricians (p < 0.0001). The pediatricians’ attitude score related to engaging physicians in medical office-based caries prevention was significantly higher than the attitude scores of the general and pediatric dentists (p < 0.05). A Spearman rank correlation analysis indicated a significant positive correlation between knowledge and practice among the general dentists (rs = 0.271, p < 0.01) and pediatricians (rs = 0.262, p < 0.01). The correlation between knowledge and attitude among the pediatricians was significantly positive (rs = 0.242, p < 0.05). Attitude and practice among the pediatricians were significantly positively correlated (rs = 0.271, p < 0.01). Pediatricians lacked ECC-related knowledge; however, they had a more positive attitude toward medical office-based prevention when they had a higher level of knowledge. Oral health-related education for pediatricians is necessary if such medical office-based caries prevention programs are to be implemented in Taiwan.