Systemic inflammation and alterations to regional cerebral blood flow (CBF) have been reported previously in obstructive sleep apnea (OSA). This study utilized arterial spin labelling (ASL) perfusion magnetic resonance imaging (MRI) to evaluate CBF in OSA patients and determine its relationship with systemic inflammation. Twenty male patients with moderate and severe OSA [apnea–hypopnea index (AHI) >15] and 16 healthy male volunteers (AHI <5) were recruited. Early- or late-phase changes in leucocyte apoptosis and its subsets were determined by flow cytometry. Perfusion MRI data were acquired with a pulsed continuous ASL technique. The CBF maps were compared using voxel-based statistics to determine differences between the OSA and control groups. The differences in CBF, clinical severity and leucocyte apoptosis were correlated. Exploratory groupwise comparison between the two groups revealed that the OSA patients exhibited low CBF values in the vulnerable regions. The lower regional CBF values were correlated with higher clinical disease severity and leucocyte apoptosis. OSA impairs cerebral perfusion in vulnerable regions, and this deficit is associated with increased disease severity. The apparent correlation between systemic inflammation and cerebral perfusion may be indicative of haemodynamic alterations and their consequences in OSA.