Increasing evidence suggests that posttraumatic stress disorder (PTSD), a serious mental health condition, is associated with physical health problems. Lipid-related molecules are crucial for central nervous system functions associated with PTSD symptoms; however, case-control studies exploring the relationship between PTSD and lipid-related molecules are scarce. We examined 68 civilian PTSD patients and 97 healthy controls, evaluating PTSD symptoms, childhood maltreatment history, suicidality, and cognitive functions. Cholesterol, triglycerides, and inflammation-related marker levels were analyzed in serum, while fatty acid levels were measured in plasma. Compared to controls, patients exhibited significantly lower high-density lipoprotein cholesterol and n-6 linoleic acid levels, alongside higher saturated palmitic acid levels and the triene-to-tetraene (T/T) ratio. PTSD symptoms, particularly hyperarousal, were significantly positively correlated with n-6 γ-linolenic, n-6 dihomo-γ-linolenic, and n-9 mead acid levels, and the T/T ratio. Cognitive functions were significantly positively correlated with n-3 docosahexaenoic acid and total n-3 fatty acid levels, and negatively correlated with saturated lauric, palmitic, and total saturated fatty acid levels. Suicidality was significantly positively correlated with dihomo-γ-linolenic acid, mead acid levels, and the T/T ratio, and negatively correlated with polyunsaturated fatty acid (PUFA) levels. Inflammation-related marker levels were significantly correlated with higher palmitic, n-9 oleic, and total n-9 fatty acid levels, and lower linoleic acid and PUFA levels. Latent profile analysis (LPA) revealed distinct subgroups associated with unique fatty acid profiles. These lipid-related alterations may improve the understanding of PTSD pathophysiology. Distinct fatty acid profiles identified by LPA may help subtype PTSD patients and guide nutrition-based personalized treatment strategies.