Pulmonary artery intimal sarcoma (PAIS) is a rare and highly aggressive form of hemangiosarcoma. The non-specific clinical manifestations, signs and routine imaging findings of this sarcoma often mimic those of pulmonary thromboembolism (PTE), resulting in frequent misdiagnosis as PTE prior to pathological confirmation in most patients. This delay in achieving an accurate diagnosis poses challenges for promptly initiating optimal treatment and further contributes to the unfavorable prognosis. The current study presents the case of a 68-year-old female who presented with acute chest tightness and dyspnea. Transthoracic echocardiography revealed the presence of atypical echogenic structures within the primary pulmonary artery, while computed tomography pulmonary angiography showed marked filling defects in the main trunk and branches of the pulmonary artery. The patient was initially misdiagnosed with PTE but did not respond well to anticoagulant therapy. Subsequent surgical resection confirmed the diagnosis of PAIS through pathological examination. Despite postoperative treatment with molecular-targeted antitumor drugs, the patient experienced tumor recurrence and intrapulmonary metastasis, ultimately succumbing to disease progression. This exceptional case is being presented to enhance the clinical understanding of PAIS, to encourage further extensive research for reliable diagnostic approaches and to provide further data that will help form efficacious therapeutic strategies to ameliorate the unfavorable prognosis of affected patients.