A previously well 59-year-old man required a prolonged intensive care unit stay due to severe COVID-19 symptoms. During the admission, he developed a cytokine storm, also known as secondary haemophagocytic lymphohistocytosis, and multiorgan failure. Despite recovering from his other organ failures, his liver function continued to deteriorate. Magnetic resonance cholangiopancreatography and subsequent endoscopic retrograde cholangiopancreatography revealed extensive intrahepatic duct dilatation with ‘beading’ but common bile duct sparing. Given the patient had no primary liver disease prior to admission, we considered secondary causes of cholestatic liver injury; this led us to an unusual diagnosis of secondary sclerosing cholangitis in critically ill patients. This case demonstrates a rare disease that has developed specifically in the context of SARS-CoV-2 infection. A review of current literature and the underlying pathophysiology for this rare disease are discussed, particularly in relation to COVID-19.