Stress is discussed as a risk factor in the manifestation and maintenance of functional somatic (FS) symptoms. However, there is a lack of evidence regarding the effects of cognitive-behavioral stress management training (CBSM) on FS symptoms and the (potentially mediating) role of the neuroendocrine system. This study aims to examine stress-related psychological and neuroendocrine changes after receiving a brief CBSM in individuals with FS symptoms. Forty-three participants of both sexes, who reported at least one current FS symptom, were analyzed (treatment group (TG) = 21, waitlist control group (WCG) = 22) using mixed models. Number of symptoms, psychological stress, and salivary cortisol levels were assessed at pretreatment, posttreatment, and 6 months later. Mixed model analyses did not reveal significant differences between the TG and the WCG regarding number of FS symptoms ( > 0.05), psychological stress measures ( > 0.05) or the cortisol awakening response (CAR) ( > 0.05). The TG presented lower diurnal cortisol levels at pretreatment, posttreatment and 6 months later ( < 0.05). We did not find significant beneficial effects that were specific to CBSM. Further research should be undertaken to investigate the effects of CBSM on real life stress or laboratory stressors in subjects with FS symptoms. Moreover, learning cognitive restructuring and establishing new coping strategies into everyday life might require more time. This study is a first step in filling the gap in understanding the influences of CBSM as a brief intervention on psychological and biological aspects of stress in participants with FS symptoms and will hopefully inform larger trials of CBSM for FS symptoms.