Military deployment increases the risk of exposure to potentially traumatising events as well as the risk of post-traumatic stress disorder and other mental illnesses. This may have adverse consequences for the family of the deployed, including negatively affecting the well-being of children. Well-being among children of formerly deployed military personnel has mainly been studied in the United States. Research from Europe and especially Scandinavian countries is scarce, and no knowledge of the well-being of children of formerly deployed military Danish personnel exists. Since 1992, Denmark has deployed more than 30,000 soldiers and other personnel to international conflicts/warzones, and at least 14% were parents when deployed. Exploiting survey data, we examined well-being among a representative sample of 1590 children (age 11 and 15) of formerly deployed Danish fathers, compared with a representative sample of 4722 children (age 11 and 15) from the background population (controls). Well-being was examined through children’s subjective well-being measured by the Strengths and Difficulties Questionnaire (SDQ), as well as through their perception of their family, self-evaluated school outcomes and relationships with friends. The analyses show that children of formerly deployed fathers, in general, are doing as well as children of the background population; however, the 11-year-old children of formerly deployed fathers are more challenged compared with children of the background population, both for subjective well-being and in having more conflicts with their parents.