To examine the characteristics and outcomes of patients with inflammatory bowel disease (IBD) hospitalized with pulmonary embolism (PE). This cross-sectional observational study analyzed data from the 2016 to 2019 National Inpatient Sample to investigate hospitalizations for PE in the USA, stratified by the presence or absence of IBD. Adult patients were selected using the International Classification of Diseases, Tenth Revision codes for PE, Crohn's disease, and ulcerative colitis. Data on patient demographics, comorbidities, and hospital characteristics were collected. Statistical analysis included univariable and multivariable logistic regression using Stata/BE 17.0, focusing on in-hospital mortality and complications in PE patients with and without IBD. Adjusted odds ratios (aOR) and their corresponding 95% confidence intervals (CI) were calculated when appropriate. PE/IBD group was younger (mean age 58.3 vs. 62.7 years; P < 0.001), had a higher proportion of white patients (81.2% vs. 70.9%; P < 0.001), and had a greater prevalence of chronic liver disease (7.54% vs. 6.02%; P = 0.002) when compared to PE/non-IBD patients. The PE/IBD group had lower prevalence rates of coronary artery disease, congestive heart failure, obesity, chronic obstructive pulmonary disease, hypertension, and diabetes. Regarding primary outcomes, there was no significant difference in in-hospital mortality between the two groups (aOR, 0.92; 95% CI, 0.77-1.09; P = 0.355). However, the IBD/PE group had a higher risk of acute kidney injury, sepsis, septic shock, cardiac arrhythmias, and deep vein thrombosis. As for secondary outcomes, PE/IBD patients had more extended hospital stays and higher healthcare costs compared with PE/non-IBD patients. Hospitalized PE patients with IBD differ demographically and have a different comorbidity profile compared to those without IBD. PE/IBD patients demonstrate greater use of healthcare resources and elevated risk of hospitalization adverse events than PE/non-IBD patients, highlighting the necessity for individualized management approaches in this population.