Few longitudinal studies have focused on mental health problems among adolescents after earthquakes. We investigated changes in post-traumatic stress symptoms (PTSS) and depressive symptoms from 18 to 31 months after the 2015 earthquake in Nepal and explored potential risk factors associated with the change in psychiatric symptoms. This study comprised of 515 adolescents, aged 11–17 years from two earthquake-affected areas, one severely affected than the other. The psychiatric symptoms were assessed using the standardized Child Post-traumatic Stress Disorder Scale and the Depression Self-Rating Scale. No significant change was observed in the prevalence of PTSS and depressive symptoms from 18 to 31 months after the earthquake. Living in severely affected area and exposure to trauma after the earthquake were associated with adolescents who developed chronic or delayed PTSS and depressive symptoms. The study findings highlight the need for disaster preparedness and early interventions that strengthen support at various levels.