BACKGROUND: A significant proportion of children in the social care system in England present with mental health problems, with the majority experiencing some form of emotional and behavioural difficulties. The most effective treatments for these children are currently unknown, partly due to a lack of robust, controlled studies. Researchers have identified a number of obstacles to conducting well-designed research with this population, making the need to test the feasibility of a randomised controlled trial especially important. METHODS/DESIGN: This protocol outlines a two-arm, randomised control feasibility trial to explore the acceptability and credibility of mentalization-based treatment (MBT) as a treatment for reducing emotional and behavioural difficulties in looked after children and to test the possibility of addressing a number of methodological challenges to conducting high-quality research with this population. MBT is a relatively new intervention which, in the adaptation of the model tested here, includes many of the features of therapy identified in NICE guidelines as necessary to support children in care. The two arms are MBT and usual clinical care (UCC). The study will take place in Hertfordshire Partnership University NHS Foundation Trust with follow-up at 12 and 24 weeks. DISCUSSION: This study will aim to ascertain whether it is worthwhile and feasible to progress to testing the intervention in a full-scale definitive randomised controlled trial (RCT). This study therefore has the potential to improve our understanding of the obstacles to conducting high-quality research with this very vulnerable population, and in the medium term, could help to improve the stability of foster placements and the emotional well-being of children in care. TRIAL REGISTRATION: ISRCTN90349442.