Abnormal levels of homocysteine (Hcy) and potassium are associated with poor prognosis of patients with ischemic stroke. Nonetheless, the roles Hcy and potassium in the prognosis of patients with acute ischemic stroke (AIS) receiving intravenous thrombolysis (IVT) with recombinant tissue-type plasminogen activator (rt-PA) are still unknown. Therefore, the purpose of this study is to investigate the association between the levels of Hcy and potassium and clinical prognosis in AIS patients receiving IVT with rt-PA. AIS patients receiving IVT with rt-PA were enrolled in this study. AIS patients were divided into early neurological deterioration (END) and no END group according to the National Institutes of Health Stroke Scale (NIHSS) scores. Moreover, patients were divided into favorable outcome and poor outcome according to the modified Rankin Scale (mRS) scores. Multivariate logistic regression analysis was applied for detecting the risk factors. Four-hundred-twenty-six patients with AIS IVT with rt-PA were recruited: 24 patients showed END within 24 h. One-hundred-fifty-seven patients showed poor outcome. Multivariate analysis showed that higher levels of Hcy level (P < 0.001) and lower levels of potassium level (P < 0.01) were more frequently in patients with END and poor outcomes in AIS patients with IVT at the three-month visit. Taken together, the high Hcy and low potassium levels may be the potential biomarker for AIS patients receiving IVT with rt-PA.