Background: The intravenous thrombolysis (IVT) with recombinant tissue plasminogen activator (rt-PA) therapy is safe and efficient during the treatment of acute ischemic stroke. Nonetheless, the different outcomes among various stroke subgroups have limited data with regard to the safety and efficacy of cryptogenic stroke (CS). The present study compared the safety and efficacy when IVT with rt-PA was used for the treatment of CS and the other stroke subtypes. Methods: This study classified the IVT with rt-PA patients within 4.5 hours after stroke onset, based on the trial of ORG 10172 in acute stroke treatment criteria in terms of diagnostic evaluation. The data were obtained from the Thrombolysis Implementation and Monitor of Acute Ischemic Stroke in China database, a large multicenter prospective registry. A multivariable logistic regression model was employed to compare the differences between the subtypes in symptomatic intracerebral hemorrhage (sICH) within 7 days and studied the mortality and the outcome during 90 days. Results: In total, 1118 patients were recruited; of these, 131 (11.7%) suffered from CS and 987 (88.3%) with the other etiology. In the CS group, patients were younger than those in the other etiology groups (P < .001). Moreover, it had a lower prevalence of previous stroke (P = .0117), receiving antiplatelet drug in 24 hours prior to thrombolysis (P = .0017), and functional independence (mRS > 1 before stroke, P = .003). The CS group had lower blood pressure (systolic blood pressure P = .0001; diastolic blood pressure; P = .0212) before thrombolysis, atrial fibrillation (P < .001), and diabetes mellitus (P = .0005). Transient ischemic attack, hypertension, hyperlipidemia, blood glucose, receiving anticoagulants in 24 hours prior to thrombolysis, and standard dosage of rt-PA were equally distributed in both groups. After the adjustment of confounders between the CS and the other subgroups, no obvious differences were observed in sICH rate and mortality (P > .05) The CS patients exhibited excellent recovery (mRS, 0-1; 63.78%) and functional independence (mRS, 0-2; 74.8%) than the large artery atherosclerosis patients. Conclusions: IVT with rt-PA is a safe and effective method for the treatment of CS patients.