•Proportions of children who met the DRIs were similar despite food neophobia status.•Food neophobia was negatively associated with protein, iron, and cholesterol intake.•Food neophobia was associated with lower intake of several micronutrients. Food neophobia is a widely prevalent eating behavior among children, which has been linked to poor dietary variety and quality. Nevertheless, data pertaining nutrient intakes in relation to food neophobia among children in Middle East countries are lacking. The present study aimed to examine the associations between food neophobia and nutrient intakes in children aged 6–12 years. A cross-sectional study of 424 children was conducted. Food neophobia among children was evaluated using the Food Neophobia Scale. Dietary data of children were collected using 24-hour dietary recalls, and nutrient densities were calculated. Intakes of macro- and micronutrients were compared to dietary recommendations. Proportions of children who met the dietary recommendations for all nutrients were similar across food neophobia groups. No significant difference in macro- or micronutrient intake was observed across categories of food neophobia in univariate analyses; however, in multiple regression models, higher food neophobia score was associated with lower protein intake (β = -0.04% of total energy, 95% CI −0.07 to −0.01), cholesterol (β = -1.79 mg/1000 kcals, 95% CI −3.51 to −0.06), potassium (β = -11.02 mg/1000 kcals, 95% CI −20.5 to −1.54), phosphorus (β = -5.30 mg/1000 kcals, 95% CI −9.74 to −0.86), magnesium (β = -1.20 mg/1000 kcals, 95% CI −2.15 to −0.25), iron (β = -0.07 mg/1000 kcals, 95% CI −0.14 to −0.01), zinc (β = -0.04 mg/1000 kcals, 95% CI −0.07 to −0.001), and selenium intake (β = -0.48 ug/1000 kcals, 95% CI −0.93 to −0.04). Our findings suggest negative associations between food neophobia in children and intake of a number of important nutrients. Further investigations are needed to identify potential factors that could influence food and nutrient intake among food neophobic children.