There is a growing interest in knowing the relationship between biological maturation and sport performance-related variables of young athletes. The objective of this study is to analyze the relationship between biological maturation, physical fitness, and kinanthropometric variables of athletes during their growing period, according to their sex. The systematic review and meta-analysis followed the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) statement and the search protocol was registered in PROSPERO, code: CRD42020208397. A search through the PubMed, Web of Sciences, and EBSCO databases was performed. A total of 423 studies were screened and 13 were included in the meta-analysis. The meta-analysis was completed by using the mean and standard deviation of each variable according to each maturation status (early, on time, or late). Differences depending on maturation were found on physical fitness, with better results in the advanced maturational groups in the male population (standard mean difference (SMD) = 0.17–2.31; p < 0.001–0.05). Differences depending on maturation were found for kinanthropometric variables in males (SMD = 0.37–2.31; p < 0.001–0.002) and height and body mass in females (SMD = 0.96–1.19; p < 0.001). In conclusion, the early maturation group showed higher values in kinanthropometric variables and better results in physical fitness, highlighting the importance of the maturational process in the talent selection programs. Despite that, more research is needed to clarify the relationship of maturation with the other variables on female populations and the changes in the muscle and bone variables during the maturation processes of both sexes.