Background As a result of the COVID-19 pandemic and the growing use of smartphones, opportunities for using digital media applications to promote health and favorable behaviors have increased. Digital methods are among those and could be used for communication between physicians and patients including text messages, images, audio, and video calls. This study aimed to investigate the use of the smartphone application (WhatsApp) to deliver oral health education to mother-child pairs, with the ultimate goal of controlling dental biofilm and caries through digital activities focused on oral hygiene. Methods This study was designed as a randomized, double-blind, parallel clinical trial involving 100 pairs of mothers and children (6–12 years old). The mothers and children will be randomly allocated to the control group (n = 50 pairs), who will receive a single visit conventional oral health education, or to the experimental group (n = 50 pairs), who will receive both a single visit conventional oral health education and educational videos through WhatsApp Messenger, twice a week. Before randomization of the groups and after the intervention, pairs will be evaluated regarding to plaque index (VPI), gingival bleeding index (GBI), and number of decayed, missing and filled permanent or primary teeth (DMF-T) modified by the inclusion of active non-cavitated carious lesions (Nyvad criteria). Socioeconomic data, dental history and oral health literacy will obtained using questionnaires (Oral Health Literacy Assessment Task for Paediatric Dentistry; BOHLAT-P). Chi-square, Student’s t-test, paired Student’s t-test, Mann-Whitney, and Wilcoxon’s sign tests were used with a 5% significance level. Discussion This intervention proposal is designed to motivate behavioral change in mother-child pairs. We hypothesize that adding digital media to traditional oral health programs will provoke improvements in oral hygiene behavior and health outcomes. To our knowledge, this is the first study evaluating the effect of educational videos communicated by digital media (WhatsApp) on the oral health of mother-child pairs evaluated by long-term dental examinations. In addition, we will assess the maternal level of comprehension of the provided information via a literacy assessment tool. The clinical trial is registered at the Brazilian Registry of Clinical Trials (No. RBR-7s8bw6m).