Background: School ergonomics is a subject of growing interest for the scientific community due to the health problems that it is associated with in students, mainly asymmetries in the spine due to the use of chairs and desks that are inadequate for their anthropometry. This study aimed to analyze the anthropometric characteristics and asymmetries among fifth- to ninth-grade students in Spain and Portugal, with the goal of obtaining data on the ideal height of seats and desks. Additionally, it evaluated the correspondence in the recommended sizes of chairs and desks according to the parameters of the European Union catalog and examined the suitability of the height as a criterion for the allocation of school furniture. Methods: Different anthropometric variables, including the height, popliteal height, shoulder-to-seat height, and elbow-to-seat height, were measured in a stratified sample of 500 students (mean age = 12.7 years, SD = 1.2) across different grades (fifth grade = 86, sixth grade = 106, seventh grade = 95, eighth grade = 89, ninth grade = 124), genders (males = 256, females = 244), and countries (Spain = 191, Portugal = 309). These measurements were used to calculate the average ideal seat and desk heights based on anthropometric formulas, which were then compared to the current furniture allocation practices. The statistical analyses included t-tests, chi-squared tests, and effect sizes, with adjustments for multiple comparisons. Results: The results revealed significant asymmetries and low correspondence in the allocation of chairs and desks of the same sizes to students, with a match rate ranging between 40% and 70%. Moreover, the correspondence was even lower when using a formula based solely on height, compared to formulas validated with specific anthropometric measures, particularly for desks, where the asymmetries reached 100% in some grades. Conclusion: These findings highlight the need to improve the adaptation of school furniture to optimize student ergonomics and comfort, and they suggest disregarding the height as the primary criterion for furniture allocation. Additionally, assigning a desk size based on the recommended chair size is discouraged.