This study investigated the effect of a school-based and teacher-led psychosocial intervention that targeted academic underachievement among conflict-affected youths. We hypothesized that participants in the intervention would experience improved school functioning and reduced levels of stress-related symptoms after the intervention, in comparison to a control group. The study was carried out in Gaza, employed a randomized control trial design, and included 300 students between 9 and 16 years of age. Students that completed the intervention reported improvement in all the domains measured after participation: better school functioning, a reduced level of stress-related symptoms, as well as long-term effects in the ability to self-regulate negative emotions, self-efficacy, better study skills, and a higher academic performance. The long-term effects were observed five months after the intervention was carried out. The implications for the implementation of psychosocial support for conflict-affected youth are discussed.