Aim <p>The current study aims to determine the estimated initiation of food allergy reactions and tolerance among different cohorts of schoolchildren, according to their school grade in Saudi Arabia during two academic years.</p> Subject and methods <p>A retrospective cohort study was conducted among screened students in the academic years 2020–2021 and 2023–2024. Included patients were schoolchildren aged 6–15 years who were screened through the school screening program. Subjects were divided according to their grade into three cohorts: 1) cohort 1 (1st and 4th grades); 2) cohort 2 (4th and 7th grades); and 3) cohort 3 (7th and 10th grades).</p> Results <p>Food allergy among the included subjects (<i>N</i> = 1,032,797) presented with a rate of 8.5 per 1000. Comparing the rate of food allergy reported by students overall during the two included academic years revealed a significant reduction (9.8 vs. 8.4 per 1000 students, respectively, percent change, 15.4%, <i>p</i>-value &lt; 0.001). Among study cohorts, cohort 1 and cohort 3 showed that food allergy reduced by 36.9% and 19.5%, respectively (<i>p</i>-value &lt; 0.01). However, food allergy was found to be increased by 2.6% in cohort 2 with no significant difference (<i>p</i>-value = 0.665). Besides, sex variation was a significant factor in food allergy tolerance.</p> Conclusion <p>This study predicted that food allergy tolerance rose significantly over among Saudi schoolchildren; yet, it was less observed among 9–12-year-olds. The outcomes highly suggest the potential influence of participants’ characteristics, including age and sex, along with possible genetic variations, on modifying biological responses.</p>