The impact of COVID-19 pandemic on mental health of adolescents are emerging and require particular attention in settings where challenges like armed conflict, poverty and internal displacement have previously affected their mental wellbeing. This study aimed to determine the prevalence of anxiety symptoms, depressive symptomatology, probable post-traumatic stress disorder and resilience in school-attending adolescents in a post-conflict area of Tolima, Colombia during the COVID-19. A cross-sectional study was carried out with 657 adolescents from 12 to 18 years old, recruited by convenience sampling in 8 public schools in the south of Tolima, Colombia, who completed a self-administered questionnaire. Mental health information was obtained through screening scales for anxiety symptoms (GAD-7), depressive symptomatology (PHQ-8), probable post-traumatic stress disorder (PCL-5) and resilience (CD-RISC-25). The prevalence observed for moderate to severe anxiety symptoms was 18.9% (95% CI 16.0–22.1) and for moderate to severe depressive symptomatology was 30.0% (95% CI 26.5–33.7). A prevalence of probable post-traumatic stress disorder (PTSD) of 22.3% (95% CI 18.1–27.2) was found. The CD-RISC-25 results for resilience had a median score of 54 [IQR 30]. These results suggest that approximately two-thirds of school-attending adolescents in this post-conflict area experienced at least one mental health problem such as anxiety symptoms, depressive symptomatology or probable PTSD during the COVID-19 pandemic. Future studies are of interest to establish the causal relationship between these findings and the impact of the pandemic. These findings highlight the challenge that schools have after pandemic to address the mental health of their students in order to promoting adequate coping strategies and implement prompt multidisciplinary interventions to reduce the burden of mental health problems in adolescents.