Primary hepatic paraganglioma (PGL) is a rare neuroendocrine tumor characterized by clinical manifestations including paroxysmal hypertension, palpitation, abdominal pain and constipation. In the present study, the case of a 21-year-old woman with pathologically confirmed hepatic PGL with megacolon following surgery is reported. The patient initially visited Beijing Tiantan Hospital (Beijing, China) for hypoferric anemia. A triple-phase CT scan of the whole abdomen showed a large hypodense mass with a solid periphery and strong arterial enhancement of the peripheral solid portion of the liver. The sigmoid colon and rectum were obviously distended, filled with gas and intestinal contents. The patient was preoperatively diagnosed with iron deficiency anemia, liver injury and megacolon and then underwent partial hepatectomy, total colectomy and enterostomy. Microscopically, the liver cells exhibited an irregular zellballen pattern. In addition, immunohistochemical staining revealed that liver cells were positive for CD56, chromogranin A, vimentin, S-100, melan-A and neuron-specific enolase. Therefore, the diagnosis of primary PGL of the liver was confirmed. These findings suggested that primary hepatic PGL should not be excluded when megacolon occurs and comprehensive imaging evaluation is of great importance for its diagnosis.