Background Internal displacement, where individuals are forced to flee their homes but remain within their country of origin, is a significant issue in conflict-affected countries like Colombia. Internally displaced (ID) adolescents experience disrupted living conditions, ongoing conflict exposure, and elevated rates of post-traumatic stress disorders (PTSD). Despite the impact of these factors on neurocognitive development, this area remains underexplored in ID adolescents. This study aims to evaluate the cognitive ability and executive functioning of Colombian ID adolescents compared to non-ID adolescents, and also examine how household income, parental education levels, and area of residence moderate the association between ID status and these skills.Method This observational case-control study will recruit two groups of adolescents (aged 12 to 16) from six high schools in a Colombian municipality affected by armed conflict. ID adolescents (n = 130) and non-ID adolescents (n = 130) will complete the Wechsler Intelligence Scale for Children-V (WISC-V) to assess cognitive ability and the 'Batería Neuropsicológica de Funciones Ejecutivas y Lóbulos Frontales-3' (BANFE-3) to assess executive functioning. Socioeconomic data will be collected from the municipal school database and a self-administered parental questionnaire. Regression analysis will be used to address the study objectives.Discussion This study will address the critical need for data on the impact of internal displacement on the cognitive and executive skills of ID adolescents. The findings will inform targeted interventions to mitigate the potential risk of cognitive impairments in these adolescents, thereby promoting their well-being, as encouraged and emphasized by international guidelines. Although this study will focus on Colombian ID adolescents, our results could benefit a broader panel of victims of internal displacement, the number of which has doubled globally in the last decade.Trial registration The study is preregistered on the Open Science Framework.