Objective: Increased arterial pulsatility index (API), usually representative of distal vascular resistance, have been linked to cerebral small vessel disease. However, their relationship with cerebral microbleeds (CMBs) is less well-studied. The present study aimed to evaluate the relationship between CMBs and API. Methods: We cross-sectionally evaluated participants from a non-clinical stroke, non-demented community-based population. APIs of cervical internal carotid and vertebral arteries were measured by ultrasonography. CMBs were assessed by susceptibility-weighted-imaging on 3T magnetic resonance imaging (MRI). Subjects were classified according to CMB locations: deep/infratentorial (DI) or strictly lobar (SL) CMB groups. DI-CMB group also included subjects with simultaneous lobar CMBs. Results: Of the 681 subjects [62.2 (8.4) years, 43.5% men] included, CMBs were found in 92 (13.5%) subjects: 57 (8.4%) with DI-CMB and 35 (5.1%) with SL-CMB. The results showed that CMB location influenced their association with API. DI-CMB was significantly associated with elevated API of internal carotid arteries (β = 0.031; 95% confidence interval = 0.002–0.059; P = 0.03), while SL-CMB was significantly associated with elevated API of vertebral arteries (β = 0.050; 95% confidence interval = 0.006–0.094; P = 0.025) in multivariate analyses adjusting for age, sex, cardiovascular risk factors, white matter hyperintensities (WMH), and lacunes. Conclusion: Our study again emphasizes (1) the association between API and cerebral small vessel disease and (2) the pathogenic differences between DI- and SL-CMBs. Our results lead to the postulation that in the presence of CMBs without clinical dysfunction yet, insidious small vascular disorders might already occur with corresponding topography.