The effect of a ketogenic diet (KD) on biochemical parameters and nutritional status has been the subject of debate over the years, as several randomized clinical trials (RCTs) obtained different results. Method: A systematic review and random-effects meta-analysis of RCTs comparing KD with a balanced diet was performed by means of a search of PubMed, Cochrane Library, Scopus, and Web of Science. Trials where the method for measuring the response variables was unclear, those that considered pathologies other than chronic non-communicable diseases and those with participants receiving pharmacological treatment for obesity were excluded from the comparison. Results: Of the studies included in the meta-analysis, no statistically significant standardized mean differences were observed for body mass index (BMI) (d = −0.457, p = 0.359), total cholesterol, COL-T (d = 0.230, p = 0.591), high-density lipoprotein, HDL (d = −0.028, p = 0.934), low-density lipoprotein, LDL (d = 0.528, p = 0.173), or triglycerides, TG (d = −0.283, p = 0.222), with high values of heterogeneity. The percentage of women included in the studies is a significant moderating variable in terms of BMI ratio (z = −6.68, p < 0.001) and TG (z = −2.27, p = 0.023). Conclusion: A KD shows no more benefits on nutritional parameters than a balanced diet, and adverse effects of being on the diet are sometimes reported.