Inflammation and infection have been noted to increase stroke risk. However, the association between septicaemia and increased risk of stroke remains unclear. This population-based cohort study, using a National Health Insurance database, aimed to investigate whether patients with septicaemia are predisposed to increased stroke risk. The study included all patients hospitalised for septicaemia for the first time between 2000 and 2003 without prior stroke. Patients were followed until the end of 2010 to evaluate incidence of stroke. An age-, gender- and co-morbidities-matched cohort without prior stroke served as the control. Cox's proportional hazards regressions were used to assess differences in stroke risk between groups. Based on hazard ratios (HRs), patients with septicaemia had greater stroke risk, especially in the younger age groups (age <45: HR = 4.16, 95% CI: 2.39-7.24, p<0.001; age 45-64: HR = 1.76, 95% CI: 1.41-2.19, p<0.001; age ≥ 65: HR = 1.05, 95% CI: 0.91-1.22, p>0.05). Haemorrhagic stroke was the dominant type (ischaemic stroke: HR = 1.20, 95% CI: 1.06-1.37, p<0.01; haemorrhagic stroke: HR = 1.82, 95% CI: 1.35-2.46, p<0.001) and patients without co-morbidities were at slightly higher risk (without co-morbidities: HR = 1.49, 95% CI: 1.02-2.17, p<0.05; with co-morbidities: HR = 1.24, 95% CI: 1.10-1.41, p<0.001). The impact of septicaemia on stroke risk was highest within 6 months of the event and gradually declined over time. Our results suggest that septicaemia is associated with an increase in stroke risk, which is greatest in haemorrhagic stroke. Closer attention to patients with history of septicaemia may be warranted for stroke preventive measures, especially for younger patients without co-morbidities.