Background: Children of parents with a mental illness or substance use disorder (COPMI) have an increased risk of developing social-emotional problems themselves. Fear of stigmatisation or unawareness of problems prevents children and parents from understanding each other. Little is known about COPMI with mild intellectual disabilities (ID), except that they have a high risk of developing social-emotional problems and require additional support. In this study, we introduce a program for this group, the effectiveness of which we will study using a quasi-experimental design based on matching. The program ‘You are okay’ consists of a support group for children and an online educational program for parents. The goal of the program is to increase children and parents’ perceived competence with an aim to prevent social-emotional problems in children. Methods/Design: Children between ten and twenty years old with mild ID (IQ between 50 and 85) and at least one of their parents with a mental illness will be included in the study. The children will receive part time treatment or residential care from an institute for children with mild ID and behavioural problems. Participants will be assigned to the intervention or the control group. The study has a quasi-experimental design. The children in the intervention group will join a support group, and their parents will be offered an online educational program. Children in the control group will receive care as usual, and their parents will have no extra offer. Assessments will be conducted at baseline, post-test, and follow up (6 months). Children, parents, and social workers will fill out the questionnaires. Discussion: The ‘You are okay’ program is expected to increase children and parents’ perceived competence, which can prevent (further) social-emotional problem development. Because the mental illness of parents can be related to the behavioural problems of their children, it is important that children and parents understand each other. When talking about the mental illness of parents becomes standard in children’s treatment, stigmatisation and the fear for stigmatisation can decrease.