Although male brains have consistently reported to be 8–10% larger than female brains, it remains not well understood whether there are differences between sexes (average or variance) in developmental trajectories. Furthermore, if sex differences in average brain growth or variance are observed, it is unknown whether these sex differences have behavioral relevance. The present longitudinal study aimed to unravel sex effects in cortical brain structure, development, and variance, in relation to the development of educationally relevant cognitive domains and executive functions (EFs). This was assessed with three experimental tasks including working memory, reading comprehension, and fluency. In addition, real-life aspects of EF were assessed with self- and parent-reported Behavior Rating Inventory of Executive Function scores. The full data set included 271 participants (54% female) aged between 8 and 29 years of which three waves were collected at 2-year intervals, resulting in 680 T1-weighted MRI scans and behavioral measures. Analyses of average trajectories confirmed general age-related patterns of brain development but did not support the hypothesis of sex differences in brain development trajectories, except for left banks STS where boys had a steeper decline in surface area than girls. Also, our brain age prediction model (including 270 brain measures) did not indicate delayed maturation in boys compared with girls. Interestingly, support was found for greater variance in male brains than female brains in both structure and development, consistent with prior cross-sectional studies. Behaviorally, boys performed on average better on a working memory task with a spatial aspect and girls performed better on a reading comprehension task, but there was no relation between brain development and cognitive performance, neither for average brain measures, brain age, or variance measures. Taken together, we confirmed the hypothesis of greater males within-group variance in brain structures compared with females, but these were not related to EF. The sex differences observed in EF were not related to brain development, possibly suggesting that these are related to experiences and strategies rather than biological development.