Forcibly displaced children often experience separation from their parents, primarily fathers. Separation can be the result of father’s death, being forced to take part in military fighting, or fleeing in search for safety elsewhere. Children who grow up in such conditions experience the severe adversities of war and displacement, as well as separation from a key attachment figure. Despite the importance of attachment figures for children’s well-being, especially during times of heightened stress, the impact of separation due to various factors related to war and displacement has received little attention in empirical work. Findings from a sample of 1544 Syrian refugee children (M_age = 10.97, SD = 2.27) living in informal settlements in Lebanon with their mothers (M_age = 38.07, SD = 8.49), of which 367 were separated from their fathers, show that father-separated children were exposed to more war-related events, and lived in worse refugee environments. Structural equation modelling shows that beyond the direct relation of war exposure and quality of the refugee environment on well-being, father separation was uniquely related to more depressive symptoms and worse self-development in children, but neither to anxiety or PTSD symptoms, nor to externalising problems. Maternal parenting did not explain the relation between father-separation and elevated depressive symptoms and poorer self-development, although it had a protective function for children’s well-being.