Patients with moyamoya disease (MMD) or intracranial atherosclerotic disease (ICAD) experience similar cerebral ischaemic events. However, MMD patients show greater angiogenesis and arteriogenesis, which play crucial roles in collateral circulation development to enhance clinical prognosis and outcome. Apelins have been associated with angiogenesis and arteriogenesis. Therefore, the aim of the present study was to determine whether apelin levels were higher in patients with MMD than in patients with ICAD or in healthy controls. We compared plasma apelin levels in 29 patients with MMD, 82 patients with ICAD, and 25 healthy participants. Twelve-hour fasting blood samples were collected and analysed using commercially available kits. Univariate analyses indicated that compared with the ICAD and healthy control groups, the MMD group had higher apelin-12, apelin-13, apelin-36, and nitric oxide levels. Binary logistic regression analyses further showed that the plasma apelin-12 level was substantially higher in MMD patients than in ICAD patients. Patients with MMD were also differentiated from patients with ICAD by their mean ages, with the former being younger. Therefore, the plasma apelin-12 level is a potential diagnostic marker for differentiating MMD and ICAD and may provide a treatment strategy for enhancing collateral circulation development and clinical prognosis and outcome.