Background Abused and neglected children are at increased risk of health problems throughout life, but negative effects may be ameliorated by nurturing family care. It is not known whether it is better to place these children permanently with substitute (foster or adoptive) families or to attempt to reform their birth families. Previously, we conducted a feasibility randomised controlled trial (RCT) of the New Orleans Intervention Model (NIM) for children aged 0–60 months coming into foster care in Glasgow. NIM is delivered by a multidisciplinary health and social care team and offers families, whose child has been taken into foster care, a structured assessment of family relationships followed by a trial of treatment aiming to improve family functioning. A recommendation is then made for the child to return home or for adoption. In the feasibility RCT, families were willing to be randomised to NIM or optimised social work services as usual and equipoise was maintained. Here we present the protocol of a substantive RCT of NIM including a new London site. Methods The study is a multi-site, pragmatic, single-blind, parallel group, cluster randomised controlled superiority trial with an allocation ratio of 1:1. We plan to recruit approximately 390 families across the sites, including those recruited in our feasibility RCT. They will be randomly allocated to NIM or optimised services as usual and followed up to 2.5 years post-randomisation. The principal outcome measure will be child mental health, and secondary outcomes will be child quality of life, the time taken for the child to be placed in permanent care (rehabilitation home or adoption) and the quality of the relationship with the primary caregiver. Discussion The study is novel in that infant mental health professionals rarely have a role in judicial decisions about children’s care placements, and RCTs are rare in the judicial context. The trial will allow us to determine whether NIM is clinically and cost-effective in the UK and findings may have important implications for the use of mental health assessment and treatment as part of the decision-making about children in the care system.