Macronutrient intake can be one of the most influential factors in cognitive and neural development in adolescents. Adolescence is a specific period of cognitive and neural development, and nutritional effects during this period could be life-long. Therefore, understanding the effects of macronutrient intake on cognitive and neural development in adolescents is crucially important. We thus examined the association across macronutrient intake, intelligence, and neural development using population-based cohort data. We conducted two studies. In study 1, we included a total of 1,734 participants (boys, 907, age [mean ± standard deviation] 171.9 ± 3.44 months; range 163.0-186.0 months) from the Tokyo TEEN Cohort (TTC) to examine the association between macronutrient intake and intelligence quotient (IQ). In study 2, we included a total of 63 participants (boys, 38, age 174.4 ± 7.7 months; range 160.7-191.6 months) to investigate the effect of nutrition intake on neural development using graph theory analysis for resting-state functional magnetic resonance imaging (rs-fMRI) derived from a subset of the TTC. TTC data revealed that a higher IQ was associated in boys with increased protein intake (β = 0.068, p = 0.031), and in girls, with reduced carbohydrate intake (β = -0.076, p = 0.024). Graph theory analysis for rs-fMRI at approximately age 12 has shown that impaired local efficiency in the left inferior frontal gyrus was associated with higher carbohydrate and fat intake ([x, y, z] = [-51, 23, 8], pFDR-corrected = 0.00018 and 0.02290, respectively), whereas increased betweenness centrality in the left middle temporal gyrus was associated with higher carbohydrate, fat, and protein intake ([x, y, z] = [-61, -43, -13], pFDR-corrected = 0.0027, 0.0029, and 0.00075, respectively). Moreover, we identified a significant moderating effect of fat and protein intake on the relationship between change in betweenness centrality over a 2-year measurement gap in the left middle temporal gyrus and intelligence (β = 12.41, p = 0.0457; β = 12.12, p = 0.0401, respectively). Our study showed the association between macronutrient intake and neural development related to intelligence in early adolescents. Appropriate nutritional intake would be a key factor for healthy cognitive and neural development.