Post-traumatic stress disorder (PTSD) is a heterogeneous mental health condition, characterized by diverse symptom profiles and biological underpinnings. A dissociative subtype of PTSD has been identified, though the potential risk factors and underlying neurobiology are yet to be understood. The current study comprised Canadian Armed Forces (CAF) members and Veterans with a history of deployment, and with diagnoses of non-dissociative (n = 31) and dissociative subtypes of PTSD (n = 19), in addition to non-deployed healthy controls (n = 14). Participants completed questionnaires assessing clinical symptoms and experiences of trauma, and provided saliva and blood samples for cortisol and inflammatory marker assessments. Individuals with dissociative PTSD displayed elevated PTSD and depression symptom severity, and greater reports of specific forms of childhood trauma compared to individuals with non-dissociative PTSD and controls. Morning cortisol was elevated in both PTSD groups compared to controls, however the PTSD groups did not differ from one another. Evening cortisol concentrations were elevated in both PTSD groups compared to controls, and in the dissociative PTSD subtype compared to the non-dissociative PTSD subtype when controlling for depression symptoms. PTSD diagnostic group moderated the relationship between awakening cortisol levels and PTSD symptom severity, such that the non-dissociative PTSD group displayed a negative correlation between awakening cortisol levels and PTSD symptom severity, while no significant relation was identified in the dissociative PTSD group. C-reactive protein (CRP) levels did not differ across diagnostic groups when accounting for body mass index (BMI). However, CRP positively correlated with depressive symptoms only among individuals with dissociative PTSD. Together, examining PTSD subtypes may help inform more effective and personalized treatment strategies in the future.