BACKGROUND: Epilepsy extends far beyond seizures; up to 80% of children with epilepsy (CWE) may have comorbid cognitive or mental health problems, and up to 50% of parents of CWE are at risk for major depression. Past research has also shown that family environment has a greater influence on children's and parents' health-related quality of life (HRQOL) and mental health than epilepsy-related factors. There is a pressing need for low-cost, innovative interventions to improve HRQOL and mental health for CWE and their parents. The aim of this randomized controlled trial (RCT) is to evaluate whether an interactive online mindfulness-based intervention program, Making Mindfulness Matter (M3), can be feasibly implemented and whether it positively affects CWE's and parents' HRQOL and mental health (specifically, stress, behavioral, depressive, and anxiety symptoms). METHODS: This parallel RCT was planned to recruit 100 child-parent dyads to be randomized 1:1 to the 8-week intervention or waitlist control and followed over 20 weeks. The intervention, M3, will be delivered online and separately to parents and children (ages 4-10 years) in groups of 4-8 by non-clinician staff of a local community epilepsy agency. The intervention incorporates mindful awareness, social-emotional learning skills, and positive psychology. It is modeled after the validated school-based MindUP program and adapted for provision online and to include a parent component. DISCUSSION: This RCT will determine whether this online mindfulness-based intervention is feasible and effective for CWE and their parents. The proposed intervention may be an ideal vector to significantly improve HRQOL and mental health for CWE and their parents given its low cost and implementation by community epilepsy agencies. TRIAL REGISTRATION: ClinicalTrials.gov NCT04020484 . Registered on July 16, 2019.