Hepatobiliary phase (HBP) images can discriminate between benign and malignant liver lesions, but it is unclear if this approach can be used in patients with Budd-Chiari syndrome (BCS). Thus, we aimed to assess the diagnostic utility of HBP images in patients with BCS. This retrospective study included all patients admitted to our institution with a diagnosis of BCS and focal liver lesions on hepatobiliary contrast agent-enhanced MR imaging (HBCA-MRI) from 2000 to 2019. MR images were reviewed by 2 radiologists blinded to the diagnosis of the lesions. Patient and lesion characteristics were recorded, focusing on HBP imaging features. Twenty-six patients (mean 35 ± 11 years old 13–65; 21 women 81% 35 ± 12 years old 13–65; 5 men 19% 36 ± 10 years old 19–44) with 99 benign liver lesions and 12 hepatocellular carcinomas (HCCs) were analyzed. Patients with HCC were significantly older than those with benign lesions (mean 50 ± 10 vs. 33 ± 9 years old, p = 0.003), with higher alpha-fetoprotein (AFP) levels (3/4 75% vs. 1/22 5% with AFP >15 ng/ml, p <0.001). Homogeneous hypointense signals were identified on HBP in 14 lesions, including 12/12 (100%) HCCs, and 2/99 (2%) benign lesions (p <0.001). Most benign liver lesions showed either peripheral (n = 52/99 53%) or homogeneous hyperintensity (n = 23/99 23%) on HBP. Lesions with signal hypointensity on HBP in patients with AFP serum levels >15 ng/ml were all HCCs. Most benign lesions showed homogeneous or peripheral hyperintensity on HBP images while all HCCs were homogeneously hypointense. HBP images are helpful to differentiate between benign lesions and HCCs and outperform other sequences. They should be systematically acquired for the characterization of focal lesions in patients with BCS. Hepatobiliary phase imaging is an approach that has recently been shown to discriminate between benign and malignant lesions in the liver. However, it was not known whether this imaging approach could be used effectively in patients with Budd-Chiari syndrome. Herein, we have shown that hepatobiliary phase imaging appears to be useful for differentiating between benign and malignant liver lesions in patients with Budd-Chiari syndrome. Display omitted •Most benign lesions showed homogeneous or peripheral hyperintensity on hepatobiliary phase images.•All HCCs were homogeneously hypointense on hepatobiliary phase images.•Hepatobiliary images are helpful to differentiate between benign lesions and HCCs in patients with Budd-Chiari syndrome.•In patients with AFP serum levels >15 ng/ml, lesions with signal hypointensity on hepatobiliary phase were all HCCs.