Annual age grouping is a common organizational strategy in academics and sports. This strategy could promote the relative effects of age, which refers to the (dis)advantages that subjects who were born in the first or last months of the year may suffer. The consequences could be minimized, resulting in better physical and/or academic results. The objective of the study was to evaluate the influence of the quarter of birth and examine the correlation between physical condition variables and academic performance. The sample included 79 students (51.90% females) 13.46 ± 0.21 years old in the second year of Obligatory Secondary Education. The physical variables of this study were explosive power, cardiorespiratory capacity, speed, flexibility, and muscle strength. They were evaluated using the horizontal jump tests, Cooper test, 50 m sprint, sit-and-reach test, and medicine ball exercises, respectively. The academic variables were obtained from the average academic grade, grouped by key competencies. An Analysis of Covariance (ANCOVA), controlling for gender, body mass, and height, revealed significant differences between male students born in the first quarter compared to those born in subsequent quarters in all physical condition variables (except for cardiorespiratory capacity). For female students, significant differences were observed only in the explosive power variable. No statistically significant intra-sex differences were evident in academic performance at any time of measurement. Additionally, moderate to large correlations were found in the physical condition and academic variables. It is concluded in relation to the need to implement diverse strategies regarding the process of developing physical conditions in adolescence that satisfy the growth needs of students based on age and sex.