Background: Childhood adversities, such as poor parental practices, exposure to violence, and risk behaviours strongly impact children’s future mental and behavioural problems. Adversities affect families living in disadvantaged environments and low- and middle-income countries (LMICs) to a greater extent than in high-income countries. Parenting programmes are an effective way to alleviate them, although their outreach and scalability is still limited in LMICs. Methods/design: A multi-site randomised controlled trial will be conducted in North Macedonia, Republic of Moldova and Romania to test the efficacy and cost-effectiveness of an optimised version of the promising Parenting for Lifelong Health Programme for Young Children (PLH-YC, 5 sessions), against a standard lecture on parenting issues (control group, 1 session). At least 864 participants who report having children between 2 and 9 years old who display elevated levels of behavioural difficulties will be randomised on a 1:1 basis to the intervention and control groups. The primary outcome will consist of parent report of child oppositional aggressive behaviour. Post-test (four months) and follow-up (12 months) assessments will provide information on short- and longer-term effects of PLH-YC compared to the parenting lecture in the control group. Discussion: This randomised trial will test the efficacy of PLH-YC in alleviating child behavioural problems and assess the cost-effectiveness, transportability across three different cultural contexts, and potential for scalability of the programme. Trial registration: ClinicalTrials.gov., Registration number: NCT04721730 (https://clinicaltrials.gov/ct2/show/NCT04721730). Registered 13.01.2021.