Background: Child mental health problems continue to be a major global concern, especially in low- and middle-income countries (LMICs). Parenting interventions have been shown to be effective for reducing child behavior problems in high-income countries, with emerging evidence supporting similar effects in LMICs. However, there remain substantial barriers to scaling up evidence-based interventions due to limited human and financial resources in such countries. Methods: This protocol is for a multi-center cluster randomized factorial trial of an evidence-based parenting intervention, Parenting for Lifelong Health for Young Children, for families with children ages 2–9 years with subclinical levels of behavior problems in three Southeastern European countries, Republic of Moldova, North Macedonia, and Romania (8 conditions, 48 clusters, 864 families, 108 per condition). The trial will test three intervention components: length (5 vs. 10 sessions), engagement (basic vs. enhanced package), and fidelity (on-demand vs. structured supervision). Primary outcomes are child aggressive behavior, dysfunctional parenting, and positive parenting. Analyses will examine the main effect and cost-effectiveness of each component, as well as potential interaction effects between components, in order to identify the most optimal combination of program components. Discussion: This study is the first factorial experiment of a parenting program in LMICs. Findings will inform the subsequent testing of the optimized program in a multisite randomized controlled trial in 2021. Trial registration: NCT03865485 registered in ClinicalTrials.gov on March 5, 2019.