Obesity can impair cardiometabolism, but low-carbohydrate diets (LCDs) may be beneficial for mitigating risk. We aimed to investigate the effects of LCDs versus low-fat diets (LFDs), under hypocaloric conditions, on flow-mediated dilation (FMD) in individuals with overweight/obesity. Secondarily, we assessed other cardiovascular markers (systolic blood pressure, diastolic blood pressure, C-reactive protein [CRP], high-density lipoprotein [HDL], low-density lipoprotein [LDL], triglycerides [TG], total cholesterol [TC]), and anthropometric and body composition measurements. PubMed, Scopus, and Web of Science were searched through May 2023 for studies involving hypocaloric LCDs versus LFDs on FMD. Meta-analyses were conducted for LCDs vs. LFDs to calculate weighted mean differences (WMD), including 10 studies reporting FMD (n = 475). Overall, hypocaloric LCDs resulted in a non-significant decrease in FMD compared with hypocaloric LFDs [WMD = -1.04% (95% CI -2.28 to 0.20), p = 0.10], while very-low-carbohydrate diets (VLCDs) significantly reduced FMD when compared with LFDs [WMD = -2.12% (95% CI: -3.35 to -0.9) p = 0.001]. LCDs did not change anthropometric and body composition measurements, nor CRP, blood pressure, HDL, or TC when compared with LFDs. However, LCDs significantly decreased TG [WMD = -19.94 mg/dL (95% CI -31.83 to -8.06), p = 0.001] and increased LDL [WMD = 20.00 mg/dL (95% CI 14.09 to 25.90), p = 0.001] when compared with LFDs. In conclusion, LCDs did not exert superior effects on cardiovascular markers or body composition when compared with LFDs in individuals with overweight or obesity, but LCDs reduced TG and increased LDL levels more than LFDs. Yet, vascular function (FMD) was reduced primarily for VLCDs.