Background: Lateral medullary infarction (LMI) is not an uncommon disease. Although lesions are usually restricted to the lateral medullary area, some patients have additional infarcts in other parts of the brain. The clinical features and prognosis of isolated LMI (pure LMI, LMIpr) have been investigated. However, it remains unclear whether clinical characteristics, prognosis and factors associated with prognosis differ between patients with LMIpr and those with additional lesions (LMI plus, LMIpl). Methods: Patients with LMI identified by MRI were enrolled. The demographic and clinical characteristics, in-hospital outcome (intensive care unit [ICU] admission, pneumonia and modified Rankin scale [mRS] at discharge), and long-term residual symptoms (vertigo/dizziness, sensory disturbances, dysphagia) and outcomes (occurrence of stroke, acute coronary syndrome [ACS], death, and mRS at follow-up) were compared between LMIpr and LMIpl patients. Factors associated with poor functional outcome (mRS 2–6) at the follow-up were analyzed. Results: Among 248 LMI patients, 161 (64.9%) had LMIpr and 87 (35.1%) had LMIpl. During admission, patients with LMIpl more frequently experienced ICU care, pneumonia and had a higher discharge mRS (3 vs. 2; p < 0.001) than LMIpr patients. The occurrence of stroke, ACS, frequency of death and functional outcome was not different during follow-up. However, residual neurologic symptoms such as dizziness (p = 0.002), dysphagia (p = 0.04) and sensory symptoms (p < 0.001) were more frequent in LMIpr than in LMIpl patients. In LMIpr patients, the rostral location of LMI was associated with poor functional outcome (p = 0.041), whereas in LMIpl patients, the presence of medial posterior-inferior cerebellar artery lesion was associated with good functional outcome (p = 0.030). Conclusion: Although the short-term outcome is poorer in LMIpl than LMIpr patients, long-term residual symptoms are more common in LMIpr patients. The location of the LMI and extra-medullary lesion affects the long-term functional outcome of LMIpr and LMIpl patients respectively.