Abstract Background Post-traumatic stress disorder is likely to affect clinical courses in the somatic hospital ward when appearing as comorbidity. Thus, this study aimed to assess the costs associated with comorbid post-traumatic stress disorder in a somatic hospital and to analyze if reimbursement appropriately compensated additional costs. Methods The study used data from a German university hospital between 2011 and 2014, analyzing 198,819 inpatient episodes. Inpatient’s episodes were included for analysis if they had a somatic primary diagnosis and a secondary diagnosis of post-traumatic stress disorder. Costs were calculated based on resource use and compared to reimbursement. Analyses were adjusted for sex, age and somatic comorbidities. Results N = 219 Inpatient’s episode were found with primary somatic disorder and a comorbid post-traumatic stress disorder. Inpatients episodes with comorbid post-traumatic stress disorder were compared to 34,229 control episodes, which were hospitalized with the same main diagnosis. Post-traumatic stress disorder was associated with additional hospital costs of €2311 [95%CI €1268 - €3355], while reimbursement rose by €1387 [€563 - €2212]. Results indicate that extra costs associated with post-traumatic stress disorder are not fully reimbursed. Male patients showed higher hospital costs associated with post-traumatic stress disorder. On average, post-traumatic stress disorder was associated with an extra length of stay of 3.4 days [2.1–4.6 days]. Conclusion Costs associated with post-traumatic stress disorder were substantial and exceeded reimbursement, indicating an inadequate reimbursement for somatic patients with comorbid post-traumatic stress disorder.