Recently, elevated levels of homocysteine and early neurological deterioration due to acute ischemic stroke have been reported to be strongly correlated. However, the role of homocysteine-lowering therapy (HLT) in the prognosis of acute ischemic stroke patients has remained unclear. This study evaluated the effects of HLT during hospitalization on the early outcomes of the 792 ischemic stroke patients with H-type hypertension from the China National Stroke Registry. The subjects were divided into HLT and non-HLT groups. Demographic and laboratory information were collected, while the functional outcome at discharge and at 90 days follow-up were assessed by National Institutes of Health Stroke Scale and modified Rankin Scale (mRS) in both groups. We found that in the univariate analysis, the proportions of patients with good functional outcomes (mRS = 0-2) were 31.68 versus 29.36 % (OR 0.90, 95 % CI 0.66-1.22, p = 0.45) at discharge and 27.02 versus 28.30 % (OR 1.06, 95 % CI 0.77-1.45, p = 0.72) at 90 days follow-up for the HLT and non-HLT groups, respectively. After multivariate analysis, there was still no significant difference in the outcomes at discharge (OR 0.85, 95 % CI 0.53-1.36, p = 0.49) or at 90 days follow-up (OR 0.98, 95 % CI 0.60-1.60, p = 0.93) for the two groups. The findings of this study indicated that patients with HLT or not during hospitalization had no significant difference in early prognosis. We concluded that HLT during hospitalization did not improve the early functional outcomes of ischemic stroke patients who also had H-type hypertension.