This study investigated the association between maternal low (<400 μg/day) or high (≥1000 μg/day) folic acid supplements (FAs) use during pregnancy and the attentional function and working memory in boys and girls at age 7–9. A longitudinal analysis based on 1609 mother–child pairs from the Spanish Infancia y Medio Ambiente Project was carried out. Multivariable regression analyses revealed that, compared to the recommended FAs use, a low FAs use during the second period of pregnancy was associated with a lower alertness in all children (β = 18.70 ms; 95% CI: 7.51; 29.89) and in girls (β = 30.01 ms; 95% CI: 12.96; 47.01), and with a lower N-back Task performance in boys (d’ number 2-back (β = −0.25; 95% CI: −0.49; 0.01)). A high FAs use throughout the two periods of pregnancy was associated with a better N-back Task performance only in girls (d’ number 2-back (β = 0.28; 95% CI: 0.01; 0.56) and d’ number 3-back (β = 0.32; 95% CI: 0.08; 0.56)). The maternal use of FAs beyond the periconceptional period may affect children’s attentional function and working memory at age 7–9 differently for boys and girls.