The school age period is characterized by significant physical and intellectual growth, necessitating the monitoring of macronutrient intake and its impact on weight and height. The objective of this study is to investigate the association between the quality and quantity of protein and fat consumption with anthropometric indices in primary school girls in Kerman. This cross-sectional analysis was conducted on primary school girls aged 6-12 (n 330) from ten schools in Kerman, Iran. A validated and reliable dish-based 185-item food frequency questionnaire was used. We calculated the amount of proteins and fats as the percentage of daily calories and grams per day. Plant-based and animal-based proteins were used to assess the protein quality. To assess the fat quality, we considered trans fatty acids (TFA), cholesterol, vegetable oils, solid vegetable oils, animal oils, omega-6 Polyunsaturated fatty acids (PUFAs), omega-3 PUFA, and (PUFAs + Monounsaturated fatty acids (MUFAs))/Saturated fatty acids (SFAs), PUFAs/SFA, and (MUFA + PUFA)/(SFA + TFA). There was a significant positive association between height-for-age z-score (HAZ) and plant protein (p < 0.001) and vegetable oils (p = 0.038) after adjustment. In higher tertiles of animal protein, weight-for-age z-score (WAZ) (p = 0.024) were significantly higher. A significant positive association was observed between omega-3 PUFA and mid-upper arm circumference (MUAC) (p = 0.039) and BMI-for-age z-score (BAZ) (p = 0.016). Our study emphasizes the importance of monitoring protein and fat intake in primary school girls for optimal growth. Positive associations were found between plant-based protein, vegetable oils and HAZ, as well as animal protein and WAZ, highlighting the impact of protein quality on growth indicators.