Background: Systemic lupus erythematosus may present with a wide variety of neurological manifestations, which could be related to the presence of vasculopathy and microembolic signals (MES). Objectives: We aimed to determine the prevalence of MES and altered blood flow velocities (BFVs) by transcranial Doppler (TCD) in patients with acute neuropsychiatric lupus erythematosus (NPLE). Methods: Fifteen consecutive patients with acute NPLE (cases) and 30 patients with systemic lupus erythematosus but without acute NPLE (controls) underwent TCD testing for comparison purposes. Results: We found higher mean BFVs in cases compared with controls in the left (100 vs. 73.5 cm/s, p = 0.018) and in the right (96 vs. 70 cm/s, p = 0.013) middle cerebral arteries. The proportion of MES in both groups was the same (13%). Abnormal TCDs were more frequent in patients with acute NPLE, 67 versus 17% (p = 0.001), and occurred more often in patients who presented seizures. Conclusions: The frequency of MES was the same in both groups; however, patients with seizures due to acute NPLE usually present with higher BFVs than controls. This could be a marker of diffuse acute cerebral vasculopathy.