Background Clostridium difficile infection (CDI) is associated with high mortality. Studies have shown an increased rate of venous thromboembolism (VTE) in patients with CDI. However, literature regarding the impact of CDI on outcomes of VTE-related hospitalizations is scarce. Our study aimed to assess the impact of CDI on inhospital outcomes among VTE hospitalizations. Methods The 2016 National Inpatient Sample (NIS) was used to identify all adult hospitalizations in the United States with a primary discharge diagnosis of acute VTE. Hospitalizations with deep vein thrombosis (DVT) or pulmonary embolism (PE) were included under VTE. The sample was stratified based on the presence or absence of active CDI. Chi-square test and weighted Student's t-test were used to analyze categorical and continuous variables, respectively. The adjusted odds ratio (OR) for clinical outcomes were calculated using multivariate logistic regression analysis. Subgroup analyses for DVT and PE hospitalizations were performed. All analyses were completed in SAS (SAS Institute Inc., Cary, NC), and a p-value of <0.05 was considered statistically significant. Results We identified 382,585 weighted hospitalizations for VTE. Among them, 0.8% had concomitant CDI. The presence of CDI was associated with a statistically significant increase in in-hospital mortality (6% vs. 3%), hospitalization cost ($147,356.5 vs. $55,193), and length of stay (13.7 vs. 5.4 days). There were more incidents of bleeding and acute respiratory failure requiring prolonged ventilation in patients with CDI. The odds of stroke were significantly higher in patients with CDI and DVT. Conclusion CDI independently increased in-hospital mortality in VTE. Preventing CDI in the VTE population may mitigate complications, improve in-hospital outcomes, and reduce treatment costs.