Previous research has shown evidence for sex differences in the neuroanatomical bases for intelligence in adults. Possible differences in the neuroanatomical correlates of intelligence and their developmental trajectories between boys and girls were investigated using functional MRI (fMRI). A large cohort of over 300 children, ages 5-18, performed the semantic processing task of silent verb generation. Regions were found in the left hemisphere exhibiting positive correlations of blood-oxygenation-level-dependent (BOLD) activation with IQ, including the middle temporal gyrus, prefrontal cortex (Broca's area), medial frontal gyrus, precuneus, and cingulate gyrus, while the superior temporal gyrus in the right hemisphere displayed a negative correlation of BOLD activation with IQ. Significant sex-X-IQ and sex-X-IQ-X-age interaction effects were also seen in the left middle temporal gyrus and left inferior frontal gyrus. Using a data-driven analysis procedure, a sex-X-IQ-X-age interaction was also demonstrated in the functional connectivity between regions in the left hemisphere, parameterized as a weighted sum of pairwise covariances between fMRI time courses. While young girls (<13 years) exhibited no correlation of connectivity with intelligence, older girls (>13 years) demonstrated a positive association of functional connectivity with intelligence. Boys, however, demonstrated the opposite developmental trajectory, from a positive association of connectivity with intelligence in young boys (ages <9 years), to a negative association in older boys (ages >13 years). Our results provide evidence for disparate neuroanatomical trajectories underlying intelligence in boys and girls.