Importance An increasing number of sexual assaults (SAs) are reported. Prior studies show that SA is associated with functional somatic disorder (FSD). Objective To investigate whether SA is associated with the development of incident FSD, including 3 functional somatic syndromes (FSSs), chronic widespread pain (CWP), irritable bowel syndrome (IBS), and chronic fatigue (CF), over 5 years. Design, Setting, and Participants A large prospective cohort study was conducted based on 5-year follow-up data (2017-2020) from the Danish Study of Functional Disorders (DanFunD). Incident FSD cases were identified through symptom questionnaires and diagnostic interviews among the population-based cohort aged 18 to 72 years from the western greater Copenhagen area. Completion of baseline SA measures and follow-up assessments was required for eligibility. Data analysis was conducted between January and September 2024. Exposures SA was assessed at baseline via 2 items from the self-reported Cumulative Lifetime Adversity Measure, dichotomized into exposed and nonexposed. Main outcomes and measures Incident FSD cases were defined using standardized criteria for single-organ and multiorgan FSD, CWP, IBS, and CF. Risk ratios (RRs) for FSD outcomes were estimated using generalized linear models adjusted for sex, emotional distress, life adversity or trauma, subjective social status, somatic comorbidities, neuroticism, health anxiety, perceived stress, and self-efficacy. Results Among the 4229 adults (53.9% women; median age, 56 [IQR, 47-64] years) from the DanFunD cohort, SA was associated with incident FSD (RR, 1.69; 95% CI, 1.17-2.44), single-organ FSD (RR, 1.65; 95% CI, 1.14-2.38), multiorgan FSD (RR, 6.47; 95% CI, 1.93-21.75), FSS (RR, 1.54; 95% CI, 1.14-2.07), and CWP (RR, 1.89; 95% CI, 1.11-3.23), while findings with IBS (RR, 1.60; 95% CI, 0.81-3.16) and CF (RR, 1.47; 95% CI, 0.89-2.42) were not significant. Overall, those who reported exposure to SA experienced a significantly higher frequency of incident somatic symptoms than individuals not exposed to SA, including musculoskeletal, gastrointestinal, cardiopulmonary, and fatigue-related symptoms. Baseline emotional distress (eg, anxiety or depression) did not modify the findings for SA and FSD. Sensitivity analysis based on diagnostic interviews confirmed these results. Conclusions and Relevance Findings of this cohort study suggest that SA may increase the risk of developing FSD, involving multiple body systems. Despite limitations from small case samples in some FSD subtypes, the pooled analysis underscores the high risk of FSD, emphasizing the critical need for further research and targeted interventions to address the long-term biopsychosocial consequences of SA.