Background: As a fibrinolytic enzyme from fermented soybean, nattokinase has been shown to be potentially beneficial for cardiovascular health, but current clinical evidences regarding the nattokinase supplementation on cardiovascular risk factors are various. This study aims to evaluate the cardiovascular efficacy of nattokinase. Methods: Four electronic databases were systematically searched to collect eligible randomized controlled trials. Data were extracted and summarized in a pre-designed form by two independent reviewers. Review Manager 5.4 software (Cochrane Library Software, Oxford, U.K.) was used for meta-analysis and bias risk assessment. Results: Six studies were eligible for quantitative analysis with 546 participants. The overall methodological quality of included studies was high. Relatively low total dosage of nattokinase had a negative effect on blood total cholesterol (MD [mean difference] = 5.27, 95% CI [confidence intervals]: 3.74 to 6.81, p 0.00001), high-density lipoprotein cholesterol (MD = –2.76, 95% CI: –3.88 to –1.64, p 0.00001), and low-density lipoprotein cholesterol (MD = 6.49, 95% CI: 0.83 to 12.15, p = 0.02). Nattokinase supplementation significantly reduced systolic blood pressure (MD = –3.45, 95% CI: –4.37 to –2.18, p 0.00001) and diastolic blood pressure (MD = –2.32, 95% CI: –2.72 to –1.92, p 0.00001), and led a slight increase in blood glucose (MD = 0.40, 95% CI: 0.20 to 0.60, p 0.0001) as compared to placebo. Nattokinase group with relatively high total dosage also had a higher total cholesterol (MD = 3.18, 95% CI: 2.29 to 4.06, p 0.00001) than control interventions, but no significant differences were found in levels of high-density lipoprotein cholesterol and low-density lipoprotein cholesterol. No significant correlation was found between nattokinase supplementation and triglyceride (p = 0.71). No notable adverse events were reported in all studies due to intake of nattokinase. Conclusions: This study further supports that nattokinase can be used as an effective adjunctive therapy for hypertension, but relatively low-dose supplementation of nattokinase may have no significant lipid-lowering effect. More work will need to be done to determine whether the positive efficacy of nattokinase on cardiovascular risk factors is dose-dependent. Systematic Review Registration: This work has been registered on PROSPERO (CRD42022315020).