Cardiorespiratory fitness (CRF) is assumed to exert beneficial effects on brain structure and executive control (EC) performance. However, empirical evidence of exercise-induced cognitive enhancement is not conclusive, and the role of CRF in younger adults is not fully understood. Here, we conducted a study in which healthy young adults took part in a moderate aerobic exercise intervention program for 9 weeks (exercise group; n = 48), or control condition of non-aerobic exercise intervention (waitlist control group; n = 72). Before and after the intervention period maximal oxygen uptake (VO2max) as an indicator of CRF, the Flanker task as a measure of EC performance and grey matter volume (GMV), as well as cortical thickness via structural magnetic resonance imaging (MRI), were assessed. Compared to the control group, the CRF (heart rate, p < 0.001; VO2max, p < 0.001) and EC performance (congruent and incongruent reaction time, p = 0.011, p < 0.001) of the exercise group were significantly improved after the 9-week aerobic exercise intervention. Furthermore, GMV changes in the left medial frontal gyrus increased in the exercise group, whereas they were significantly reduced in the control group. Likewise, analysis of cortical morphology revealed that the left lateral occipital cortex (LOC.L) and the left precuneus (PCUN.L) thickness were considerably increased in the exercise group, which was not observed in the control group. The exploration analysis confirmed that CRF improvements are linked to EC improvement and frontal grey matter changes. In summary, our results support the idea that regular endurance exercises are an important determinant for brain health and cognitive performance even in a cohort of younger adults.