Abstract Objective Transcranial Doppler (TCD) and brain MRI (Magnetic Resonance Imaging) may be useful in evaluating patients with antiphospholipid syndrome (APS), helping to stratify the risk of cerebrovascular ischemic events in this population. This study aimed to assess the frequency of brain MRI abnormalities in patients with primary antiphospholipid syndrome (PAPS), secondary antiphospholipid syndrome (SAPS), and systemic lupus erythematosus (SLE) and correlate to TCD findings. Methods The study, conducted over four years at two autoimmune disease referral centers, included 22 PAPS patients, 24 SAPS patients, 27 SLE patients without APS, and 21 healthy controls. All participants underwent TCD to assess cerebral hemodynamics, detect microembolic signals, and evaluate right-to-left shunts, followed by brain MRI and magnetic resonance angiography. MRI scans were reviewed for acute microembolism, localized cortical infarctions, border infarctions, lacunar infarctions, ischemic lesions, white matter hyperintensity, micro and macro hemorrhages, and arterial stenosis ≥50% of the cervical carotid artery, by two neuroradiologists blinded to the clinical data. Results Brain MRI findings were similar between the groups, except for lacunar infarction, more frequent in patients with SAPS (p = 0.022). Patients with intracranial stenosis detected by TCD had a higher frequency of territorial infarction (40% vs.s 7.5%, p = 0.02), lacunar (40% vs.s 11.3%, p = 0.075), and borderzone infarcts (20% vs.s 1.9%, p = 0.034). Conclusions Patients with intracranial stenosis presented a higher frequency of territorial, lacunar, and borderzone infarcts, suggesting that evaluating the intracranial vasculature should not be neglected in patients with APS and stroke.