Background: Since 1967, the Palestinian Occupied Territories are marked by a protracted political conflict. During this conflict, about one fifth of the Palestinian population has been detained; a considerable part of them having children outside prison. Although parental detention negatively impacts children’s psychological wellbeing, little is known about this impact within contexts of protracted armed conflict. Therefore, this study aimed at gaining insight into the impact of parental detention onto adolescents’ psychological well-being. Method: Of 314 (11- to 18-year old) Palestinian adolescents who took part, the fathers of 204 adolescents were detained in Israeli prisons. The adolescents completed two self-report questionnaires: the UCLA-PTSD-Reaction Index, investigating symptoms of posttraumatic stress, and the Strengths and Difficulties Questionnaire, looking at overall psychological problems. Several hierarchical regression analyses investigated mental health differences between both the groups, and possible associations between sociodemographic characteristics and the witnessing of the father’s arrest, and the mental health outcomes. Results: Parental detention largely impacted adolescents’ mental health, with one fifth to two thirds of the adolescents reporting considerable mental health problems. Witnessing the arrest of the father even increased this risk considerably. Above, girls, younger adolescents, participants living in refugee camps, and those living with extended families also reported higher scores on both questionnaires. Conclusions: Detention of fathers in the context of protracted armed conflicts has a large impact on adolescents’ mental health. Besides an overall plea to end armed conflicts as fast as possible, the study also delineates considerable implications for the support and care for these adolescents and their families.