Background and purpose: Increased supratentorial white matter hyperintensities volume (S-WMHV) has been reported to be a predictor of worse outcome in patients with acute ischemic stroke (AIS). However, few studies have focused on less common locations, such as brainstem white matter hyperintensities (B-WMH), and their relationship to S-WMHV. This study aimed to examine whether B-WMH affect clinical outcome after AIS or transient ischemic attack (TIA). Methods: Based on magnetic resonance imaging evidence, B-WMH were evaluated in 313 prospectively identified patients with AIS/TIA and registered as absent or present. Standardized S-WMHV was quantified using a validated volumetric image analysis and natural log-transformed (Log_S-WMHV). Poor outcome was defined as a modified Rankin Scale score of 3–6 at 3 months after the index event. Results: Brainstem white matter hyperintensities were detected in 57 (18.2%) patients. In unadjusted analyses for outcome, the presence of B-WMH was associated with worse outcome, compared with patients without B-WMH (P = 0.034). In multivariate analysis controlling for age, atrial fibrillation, stroke severity, reperfusion therapies and Log_S-WMHV, only B-WMH [odds ratio (OR), 2.46; P = 0.021] and stroke severity (OR, 1.23; P < 0.001) remained independently associated with unfavourable 90-day modified Rankin Scale score. Patients with B-WMH were older (OR, 1.06; P < 0.001) and tended to have more hyperlipidaemia (OR, 2.21; P = 0.023) and peripheral arterial disease (OR, 2.57; P = 0.031). Conclusions: Brainstem white matter hyperintensities are an independent predictor of poor outcome after AIS/TIA and this relationship persists after adjustment for important prognostic factors. Our results also show that leukoaraiosis in this location identifies patients with a specific risk factor profile, suggesting differences in the underlying pathogenesis.