The pre-season period in basketball includes all the physiological attributes that the players need to work on and develop, in order to sustain a full season workload. The monitoring of the effectiveness of pre-season training is based on a variety of biochemical and physiological indices; however, it is still unclear how pre-season training affects those markers. Therefore, this study aimed to analyze the effects of pre-season training on biochemical and physiological markers. A search was performed in five large scientific databases (Pubmed (Medline), Scopus, Science-Direct, Sport-Discus (EBSCO), Semantic Scholar) and produced 7081 results, which after removing duplicates and applying inclusion and exclusion criteria, resulted in 28 published scientific articles being included in this review. The most important findings suggested that the majority of the studies used a 6- or an 8-week pre-season training protocol, because these protocols have shown significant positive effects over the years. In addition, the plyometric training protocols that were used by many studies have been found to be beneficial for basketball athletes for many physiological parameters. Furthermore, the evaluation of biochemical markers can be a very useful tool in monitoring and managing fatigue, which is an essential part of modifying the training process, in order to maximize performance.