Angiomyxoma (AM) occurs almost exclusively in the soft tissues of the pelvic and perineal regions. AM is a highly uncommon condition that can be easily misdiagnosed when it is present in other regions of the body. The current study presents a case in which AM of the liver coexisted with focal nodular hyperplasia (FNH). A 56-year-old woman presented with two space-occupying lesions of the liver without any other clinical symptoms, and it was not easy to definitively diagnose the two intrahepatic lesions by imaging examinations. Due to the low incidence of AM in the liver, precise and clear clinical information on the condition is still unavailable, and the lesion was initially misdiagnosed as other hepatic tumors preoperatively. Once a tumor resection had been performed, a histopathological examination revealed that the microscopic features of the lesions were consistent with those of AM and FNH. The patient was followed up for 1 year, and no recurrence or metastasis was found. Surgical excision is an effective treatment for AM, and long-term follow-up is essential due to the risk of recurrence. The joint presentation of AM and FNH is rare in clinical practice, and although FNH of the liver is commonly reported, the difficulty of diagnosis increases when both conditions occur at the same time. Therefore, it is necessary to assist clinicians in making informed decisions regarding diagnosis and treatment.