An increasing number of sexual assaults (SAs) are being reported. This study investigated associations between SA and FSD, conceptualized as bodily distress syndrome (BDS), and five functional somatic syndromes (FSSs): chronic widespread pain (CWP), irritable bowel (IB), chronic fatigue (CF), multiple chemical sensitivity (MCS), and whiplash-associated disorder (WAD). Participants (n = 7493) from the population-based cohort Danish Study of Functional Disorders (DanFunD) completed questionnaires on FSD, emotional distress, SA, and sociodemographics. Risk ratios (RRs) for each FSD and emotional distress were calculated in nine models with SA as the primary exposure using generalized linear models with binomial family and log link and were adjusted for other potential risk factors. The results showed that SA was associated with single-organ FSD (RR = 1.51; 95% CI = 1.22–1.87), multi-organ FSD (RR = 3.51; 95% CI = 1.89–6.49), CWP (RR = 1.28; 95% CI = 0.83–1.98), IB (RR = 2.00; 95% CI = 1.30–3.07), CF (RR = 1.81; 95% CI = 1.42–2.32), WAD (RR = 2.62; 95% CI = 1.37–5.03), MCS (RR = 3.04; 95% CI = 1.79–5.17), emotional distress (RR = 1.75; 95% CI = 1.21–2.54), and health anxiety (RR = 1.65; 95% CI = 1.10–2.46). Overall, SA victims experienced significantly more somatic symptoms than individuals not exposed to SA. Adjusting for physical and emotional abuse did not change the observed associations. Our results suggest a large impact of SA on the overall somatic and mental health of SA victims. Due to the cross-sectional study design, further studies are required.