Refugees are a special population who experience adversity before, during and after forced displacement. Hence, many of them show post-traumatic stress symptoms (PTSS). PTSS can be transmitted from the mother to the child and are associated with alterations in cortisol responses. Positive parenting practices, such as maternal affection, counteracts psychopathology in early childhood. The aim of this explorative study was to investigate how children's cortisol is associated with mothers' cortisol after forced displacement, and whether or not an association depends on maternal affection. A total of 42 Arabic-speaking mother-child dyads, who came to Germany as refugees from Syria or Iraq within the past four years, participated in the present cross-sectional study. All children were below the age of 5 years. We assessed children's and mothers' hair cortisol concentration (HCC) and PTSS. Additionally, we observed and objectively rated maternal affection during mother-child interactions. The association between mothers' and children's HCC, as well as their associations with maternal affection, depended on the difference between children's and mothers' HCC. Furthermore, this HCC difference significantly predicted children's PTSS. Hence, in order to understand the mechanisms underlying children's PTSS, it is essential to consider maternal variables and differential effects within samples. We discussed possible explanations for those findings.