There is strong evidence that ceramides play a significant role in the pathology of inflammatory bowel disease (IBD) and chronic liver injury. Long-chain (LC) and very long-chain (VLC) ceramides have opposing functions, yet the associations of circulating levels of ceramide species in patients with IBD and primary sclerosing cholangitis (PSC)—as inflammatory biliary-hepatic disease closely linked to IBD— with disease severity remain poorly studied. This study investigates whether serum levels of ceramide (Cer) and hexosylceramide, a glycated ceramide derivative, are associated with disease severity in these conditions. Serum levels of eight ceramide and five hexosylceramide species were measured in 16 healthy controls, 57 patients with IBD, 7 patients with PSC, and 13 patients with PSC-IBD. Lipid levels were determined using direct flow injection analysis with a triple quadrupole mass spectrometer. Patients with IBD exhibited higher levels of Cer 18:1;O2/16:0 and Cer 18:1;O2/18:0 compared to controls. Their LC/VLC ceramide ratio was elevated and positively correlated with C-reactive protein and fecal calprotectin. However, ceramide and hexosylceramide levels were not associated with stool consistency, disease localization, or extra-intestinal manifestations. Patients with PSC and PSC-IBD also had increased LC/VLC ceramide ratios, primarily due to a decline in VLC ceramide species. In PSC-IBD, this ratio correlated positively with cholestasis markers. Additionally, serum hexosylceramide 18:1;O2/16:0 and 24:1 levels were specifically elevated in PSC. This study demonstrates that an altered LC/VLC ceramide balance is associated with disease severity in IBD, PSC-IBD, and PSC, highlighting its potential as a biomarker for IBD, PSC-IBD, and PSC. As our PSC cohorts were small, a confirmatory study is required.