Venous thromboembolism (VTE) represents one of the most common and life-threatening extraintestinal complications of inflammatory bowel disease (IBD). Therefore, the prevention of VTE is essential and foremost involves the assessment of individual patient risk factors for VTE and, consequently, the correction of those risk factors that are modifiable. Mechanical and pharmacological prophylaxis are highly effective at preventing VTE in patients hospitalized for acute disease, and they are recommended by the leading guidelines for hospitalized patients with IBD. Unfortunately, several recent surveys reported that prophylaxis against VTE is still poorly implemented because of concerns about its safety and a lack of awareness of the magnitude of thrombotic risk in patients with IBD. Therefore, further efforts are required to increase the thromboprophylaxis rate in these patients to bridge the gap between the best care and standard care and, consequently, to avoid preventable VTE-associated morbidity and mortality. This review provides insight on the critical points that persist on the prevention and treatment of VTE in patients with IBD.