Subconjunctival hemorrhage (SCH) is a benign eye condition that is often noticeable and leads to medical attention. Despite previous studies investigating the relationship between SCH and cardiovascular diseases, the relationship between SCH and bleeding disorders remains controversial. In order to gain further insight into this association, a nationwide cohort study was conducted using data from the National Health Insurance Service-National Sample Cohort version 2.0 from 2006 to 2015. The study defined SCH using a diagnostic code and compared the incidence and risk factors of intracerebral hemorrhage (ICH) and gastrointestinal (GI) bleeding in 36,772 SCH individuals and 147,088 propensity score (PS)-matched controls without SCH. The results showed that SCH was associated with a lower risk of ICH (HR = 0.76, 95% CI = 0.622–0.894, p = 0.002) and GI bleeding (HR = 0.816, 95% CI = 0.690–0.965, p = 0.018) when compared to the PS-matched control group. This reduced risk was more pronounced in females and in the older age group (≥ 50 years), but not observed in males or younger age groups. In conclusion, SCH dose not increase the risk of ICH and major GI bleeding and is associated with a decreased incidence in females and individuals aged ≥ 50 years.