Fall dormancy (FD) is an essential trait to overcome winter damage and for alfalfa (Medicago sativa) cultivar selection. The plant regrowth height (PRH) after autumn clipping is an indirect way to evaluate FD. Transcriptomics, proteomics, and QTL mapping have revealed crucial genes correlated with FD, however, these genes can’t predict alfalfa FD very well. Here, we conducted genomic prediction of FD using whole genome SNP markers based on machine learning-related methods support vector machines (SVM) regression and regularization-related methods, such as lasso and ridge regression. The results showed that using SVM regression with linear kernel and the top 3,000 GWAS-associated markers achieved the highest prediction accuracy for FD of 64.1%. For RPH, the prediction accuracy was 59.0% using the 3,000 GWAS-associated markers and the SVM linear model. It is better than that using whole-genome markers (25.0%). Therefore, the method we explored for alfalfa FD prediction outperformed the other models, such as lasso and ElastNet. The study suggests the feasibility of using machine learning to predict FD with GWAS-associated markers, and the GWAS-associated markers combined with machine learning would benefit FD-related traits as well. Application of the methodology may provide potential targets for FD selection, which would accelerate genetic research and molecular breeding of alfalfa with optimized FD.