Background An individual education plan (IEP) is a key element in the support of the schooling of children with special educational needs or disabilities. The IEP process requires effective communication and strong partnership between families, school staff, and health care practitioners. However, these stakeholders often report their collaboration as limited and difficult to maintain, leading to difficulties in implementing and monitoring the child’s IEP. Objective This paper aims to describe the study protocol used to evaluate a technological tool (CoEd application) aiming at fostering communication and collaboration between family, school, and health care in the context of inclusive education. Methods This protocol describes a longitudinal, nonrandomized controlled trial, with baseline, 3 month, and 6-month follow-up assessments. The intervention consisted of using the web-based CoEd application for 3 months to 6 months. This application is composed of a child’s file in which stakeholders of the support team can share information about the child’s profile, skills, aids and adaptations, and daily events. The control group is asked to function as usual to support the child in inclusive settings. To be eligible, a support team must be composed of at least two stakeholders, including at least one of the parents. Additionally, the pupil had to be aged between 10 years and 16 years, enrolled in secondary school, be taught in mainstream settings, and have an established or ongoing diagnosis of autism spectrum disorder, attention-deficit/hyperactivity disorder, or intellectual disability (IQ&lt;70). Primary outcome measures cover stakeholders’ relationships, self-efficacy, and attitudes toward inclusive education, while secondary outcome measures are related to stakeholders’ burden and quality of life, as well as children’s school well-being and quality of life. We plan to analyze data using ANCOVA to investigate pre-post and group effects, with a technological skills questionnaire as the covariate. Results After screening for eligibility, 157 participants were recruited in 37 support teams, composed of at least one parent and one professional (school, health care). In September 2023, after the baseline assessment, the remaining 127 participants were allocated to the CoEd intervention (13 teams; n=82) or control condition (11 teams; n=45). Conclusions We expect that the CoEd application will improve the quality of interpersonal relationships in children’s IEP teams (research question [RQ]1), will show benefits for the child (RQ2), and improve the well-being of the child and the stakeholders (RQ3). Thanks to the participatory design, we also expect that the CoEd application will elicit a good user experience (RQ4). The results from this study could have several implications for educational technology research, as it is the first to investigate the impacts of a technological tool on co-educational processes. International Registered Report Identifier (IRRID) DERR1-10.2196/63378< Réduire