Purposes Recently, artificial intelligence has been used to determine sex using fundus photographs alone. We had earlier reported that sex can be distinguished using known factors obtained from color fundus photography (CFP) in adult eyes. However, it is not clear when the sex difference in fundus parameters begins. Therefore, we conducted this study to investigate sex determination based on fundus parameters using binominal logistic regression in elementary school students. Methods This prospective observational cross-sectional study was conducted on 119 right eyes of elementary school students (aged 8 or 9 years, 59 boys and 60 girls). Through CFP, the tessellation fundus index was calculated as R/(R + G + B) using the mean value of red-green-blue intensity in the eight locations around the optic disc. Optic disc ovality ratio, papillomacular angle, retinal artery trajectory, and retinal vessel were quantified based on our earlier reports. Regularized binomial logistic regression was applied to these variables to select the decisive factors. Furthermore, its discriminative performance was evaluated using the leave-one-out cross-validation method. Sex difference in the parameters was assessed using the Mann-Whitney U test. Results The optimal model yielded by the Ridge binomial logistic regression suggested that the ovality ratio of girls was significantly smaller, whereas their nasal green and blue intensities were significantly higher, than those of boys. Using this approach, the area under the receiver-operating characteristic curve was 63.2%. Conclusions Although sex can be distinguished using CFP even in elementary school students, the discrimination accuracy was relatively low. Some sex difference in the ocular fundus may begin after the age of 10 years.