Maturation of cognitive control abilities has been attributed to the protracted structural maturation of underlying neural correlates during adolescence. This study examined the relationship between development of two forms of cognitive control (proactive and reactive control) and structural maturation of the ACC, dorsolateral pFC, and ventrolateral pFC (vlPFC) between early and mid adolescence using a longitudinal design. Adolescents ( n = 92) underwent baseline assessments when they were 12 years old and follow-up assessments approximately 4 years later. At each assessment, structural MRI scans were acquired, and a modified Stroop task was performed. Results showed longitudinal improvements in reactive control between early and mid adolescence. Furthermore, magnitude of the improvement in proactive control was associated with reduced thinning of the right vlPFC across the sample, whereas the magnitude of the improvements in reactive control was associated with reduced thinning of the left ACC in men alone. These findings suggest that individual differences in the maturation of ACC and vlPFC underlie the development of two distinct forms of cognitive control between early and mid adolescence as well as highlight sex differences in this relationship.