Milk fermented with specific lactic acid bacteria (LAB) was reported to be a rich source of metabolites, such as peptides with different biological activities that may have a positive effect on cardiovascular health. Thus, in this study, the antithrombotic and hypocholesterolemic activities of fermented milk with specific strains of Lactococcus lactis were investigated before and after exposure to a simulated gastrointestinal digestion (SGD) model. The inhibition of thrombin-induced fibrin polymerization (IC50 peptide concentration necessary to inhibit thrombin activity by 50%), anticoagulant activity, inhibition of micellar solubility of cholesterol and bile acid binding capacity of water soluble fractions (WSF) <3 kDa from fermented milk were evaluated. Results indicated that the WSF from fermented milk with Lc-572 showed antithrombotic (IC50 = 0.049 mg/mL) and hypocholesterolemic (55% inhibition of micellar solubility of cholesterol and 27% bile acid binding capacity) activities. Meanwhile, fermented milk with Lc-571 showed mainly antithrombotic activity (IC50 = 0.045 mg/mL). On the other hand, fermented milk with Lc-600 presented mainly hypocholesterolemic activity (31.4% inhibition of micellar solubility of and 70% bile acid binding capacity). Moreover, biological activities were not lost after simulated gastrointestinal digestion conditions. Thus, fermented milk with these specific L. lactis strains show potential for the development of functional foods.