Little insight exists into sex differences in diagnostic trajectories for common somatic symptoms. This study aims to quantify sex differences in the provided primary care diagnostic interventions for common somatic symptoms, as well as the consequences hereof for final diagnoses. In this observational cohort study, we used real-world clinical data from the Dutch Family Medicine Network (N = 34,268 episodes of care related to common somatic symptoms; 61,4% female). The association between patients' sex on the one hand, and diagnostic interventions and disease diagnoses on the other hand, were assessed using multilevel multiple logistic regression analyses. Structural equation modelling was used to estimate a mediation model with multiple parallel mediators to assess whether the fewer disease diagnoses given to female patients were mediated by the fewer diagnostic interventions female patients receive, compared to male patients. Women received fewer physical examinations (OR = 0.84, 95%CI = 0.79–0.89), diagnostic imaging (OR = 0.92, 95%CI = 0.84–0.99) and specialist referrals (OR = 0.85, 95%CI = 0.79–0.91) than men, but more laboratory diagnostics (OR = 1.27, 95%CI = 1.19–1.35). Women received disease diagnoses less often than men for their common somatic symptoms (OR = 0.94, 95%CI = 0.89–0.98). Mediation analysis showed that the fewer disease diagnosis in female patients were mediated by the fewer diagnostic interventions conducted in women compared to men. This study shows that sex inequalities are present in primary care diagnostic trajectories of patients with common somatic symptoms and that these lead to unequal health outcomes in terms of diagnoses between women and men. FPs have to be aware of these inequalities to ensure equal high-quality care for all patients. •Sex differences exist in diagnostic trajectories of patients with somatic symptoms.•Men with somatic symptoms receive more primary care diagnostic interventions than women.•Fewer diagnostic interventions mediate fewer disease diagnoses in women.•FPs should be aware of these sex inequalities to provide equal care for all patients.