Abstract Background Portal vein thrombosis (PVT) is known to occur frequently in patients with inflammatory bowel disease (IBD), particularly when compounded by factors such as abdominal infection, IBD flares, or intra-abdominal surgery. However, PVT can lead to diverse complications, causing acute issues like intestinal ischemia or necrosis and long-term problems such as portal hypertension, varices, and ascites. Nevertheless, there is a significant shortage of research regarding the characteristics and prognosis of PVT in the context of IBD. Particularly, with the rising prevalence of IBD patients in Asia, the authors conducted an evaluation of clinical presentation and prognosis of PVT in IBD patients at a large tertiary hospital in South Korea. Methods This study is a retrospective study conducted at a single tertiary center in South Korea. It examined patients aged 18 and above diagnosed with inflammatory bowel disease (IBD) who had confirmed portal vein thrombosis (PVT) between June 1, 1989, and December 15, 2021. The study focused on investigating patient characteristics, PVT characteristics, treatment methods, and outcomes. The diagnosis and resolution of PVT were confirmed using enhanced CT imaging. Results A total of 78 patients met the inclusion criteria for this study. Only 21% (16/78) received oral anticoagulants, yet nearly all patients (96%; 75/78) achieved Complete Radiologic Resolution (CRR). When comparing baseline characteristics between the anticoagulation use group and the non-use group, a trend was observed with a higher utilization of anticoagulants in cases where the main portal vein was involved rather than only the left or right portal vein (p-value 0.006). However, when conducting multivariable analysis, no factors significantly influenced CRR, especially anticoagulant use and surgery status. Conclusion PVT concomitant with IBD demonstrated favorable outcomes regardless of anticoagulation use.