There is a large body of literature reporting the prognostic factors for a positive outcome of neurorehabilitation performed in the subacute phase of stroke. Despite the recent development of algorithms based on neural networks or cluster analysis for the identification of these prognostic factors, the literature lacks a rigorous comparison among classical regression, neural network, and cluster analysis. Moreover, the three methods have rarely been tested on a sample independent from that in which prognostic factors have been identified. This study aims at providing this comparison on a wide sample of data (1522 patients) and testing the results on an independent sample (1000 patients) using 30 variables. The accuracy was similar among regression, neural network, and cluster analyses on the analyzed sample (76.6%, 74%, and 76.1%, respectively), but on the test sample, the accuracy of neural network decreased (70.1%). The three models agreed in identifying older age, severe impairment, unilateral spatial neglect, and total anterior circulation infarcts as important prognostic factors. The binary regression analysis also provided solid results in the test sample, especially in terms of specificity (81.8%). Cluster analysis also showed a high sensitivity in the test sample (82.6%) and allowed a meaningful easy-to-use classification tree to be obtained.