Objective: To explore whether deep medullary veins (DMVs) in the unaffected hemisphere were associated with functional outcome in acute cardioembolic stroke patients. Methods: Acute cardioembolic stroke patients at a single center were retrospectively included. DMVs visibility in the unaffected hemisphere was assessed using a well-established four-grade scoring method based on susceptibility-weighted imaging (SWI): grades 0–3 (grade 0 for no visible DMVs; grade 1 for the numbers of conspicuous DMVs < 5; grade 2 for numbers raging from 5 to 10; grade 3 for more than 10). Patients were further divided into mild-to-moderate (grade 0–2) and severe DMVs (grade 3) groups. Functional outcomes were evaluated using the modified Rankin scale (mRS) score at three months. Poor outcome was defined as mRS ≥ 3. Binary logistic regression analysis was used to explore the association between DMVs grade and functional outcome. Results: A total of 170 patients were finally included. Compared with the mild-to-moderate DMVs group (149 patients), the severe DMVs group (21 patients) had higher baseline National Institutes of Health Stroke Scale (NIHSS) scores (p = 0.002), lower levels of admission systolic blood pressure (BP) (p = 0.031), and elevated rates of large infarction (p = 0.003). At three months, the severe DMVs group had higher mRS (p = 0.002). Patients in the poor outcome group (82/170, 48.2%) had older age, higher baseline NIHSS score, lower admission diastolic BP, higher rates of hemorrhagic transformation and large infarction, and an increased proportion of severe DMVs (all p < 0.05). After adjusting for confounders, multivariable regression analysis showed that the severe DMVs grade (adjusted odds ratio [OR] = 5.830, 95% confidence interval [CI] = 1.266–26.856, p = 0.024) was significantly associated with three-month functional outcomes without interaction with other potential risk factors (p for interaction > 0.05). Conclusions: DMVs grade in the unaffected hemisphere was independently associated with three-month functional outcome in acute cardioembolic stroke patients. Patients with severe DMVs were more likely to have a poor functional outcome at three months.