(1) Background: The purpose of the current meta-analysis was to investigate any positive or negative effects of ketogenic diets in athletes and provide an assessment of the size of these effects. (2) Methods: Databases were used to select relevant studies up to January 2021 regarding the effects of ketogenic diets in athletes. Inclusion criteria were as follows: data before and after ketogenic diet use, being randomized controlled trials and presenting ketogenic diets and assessments of ketone status. Study subjects were required to be professional athletes. Review studies, pilot studies, and studies in which non-athletes were included were excluded from this meta-analysis. The outcome effect sizes in these selected studies were calculated by using the standardized mean difference statistic. (3) Results: Eight studies were selected for this meta-analysis. Athletes who consumed the ketogenic diet had reduced body fat percentages, respiratory exchange rates, and increased total cholesterol compared to athletes who did not consume this diet. However, body mass index, cardiorespiratory fitness, heart rate, HDL cholesterol, glucose level, and insulin level were unaffected by the diet. (4) Conclusions: Ketogenic diets had a beneficial effect by decreasing body fat percentage, but athletes with high total cholesterol level need to be monitored when instituting a ketogenic diet. Our study sample size was limited; therefore, additional studies may be needed to confirm the current findings. Further studies need to be conducted on changes in LDL cholesterol, HDL cholesterol, total cholesterol and ratio of LDL to HDL cholesterol.