(1) Background: Larger blood pressure variability (BPv) in the first 3 h post-stroke onset increases pathophysiological effects such as infarct size, and leads to greater risk of disability, comorbidities and mortality at 90 days. However, there is limited information on the relationship between systemic and cerebral haemodynamic and variability parameters. (2) Objectives: This study determined the effect of a gradual change in head position (GHP) on cerebral blood flow velocity variability (CBFVv) and mean arterial blood pressure variability (MABPv), in healthy controls and acute ischaemic stroke (AIS) patients. Methods: CBFVv and MABPv were expressed as standard deviation (SD) and coefficient of variation. A total of 16 healthy controls (mean age 57 ± 16 years) were assessed over two visits, 12 ± 8 days apart, and 15 AIS patients (mean age 69 ± 8.5 years) were assessed over three visits (V1: 13.3 ± 6.9 h, V2: 4.9 ± 3.2 days and V3: 93.9 ± 11.5 days post-stroke). (3) Results: In response to GHP, MABPv does not initially increase, but over time MABPv showed a significant increase in response to GHP in AIS (visits 2 and 3) and controls (visit 2). Additionally, in response to GHP in AIS, CBFVv increased in the affected hemisphere. Lastly, in AIS, a significant correlation between CBFVv and MABPv, assessed by SD, was seen in the unaffected hemisphere, whereas this relationship was not demonstrated in the affected hemisphere. (4) Conclusions: To our knowledge, this is the first study to analyse the relationship between CBFVv and MABPv. Shedding light on the effect of head position on the relationship between cerebral blood flow and blood pressure is important to improve our understanding of the underlying effects of cerebral autoregulation impairment. This early mechanistic study provides evidence supporting supine head positioning in healthy controls and stroke patients, through demonstration of a reduction of MABPv and increase in CBFVv.