Top-down attentional control seems to increase and suppress the activity of sensory cortices for relevant stimuli and to suppress activity for irrelevant ones. Higher physical activity (PA) and aerobic fitness (AF) levels have been associated with improved attention, but most studies have focused on unimodal tasks (e.g., visual stimuli only). The impact of higher PA or AF levels on the ability of developing brains to focus on certain stimuli while ignoring distractions remains unknown. The aim of this study was to examine the neural processes in visual and auditory sensory cortices during a cross-modal attention-allocation task using magnetoencephalography in 13 to 16 years old adolescents (n = 51). During continuous and simultaneous visual (15 Hz) and auditory (40 Hz) noise-tagging stimulation, participants attended to either visual or auditory targets appearing on their left or right sides. High and low PA groups were formed based on seven-day accelerometer measurements, and high and low AF groups were determined based on the 20-m shuttle-run test. Steady-state (evoked) responses to the visual stimulus were observed in all the adolescents in the primary visual cortex, but some did not show responses in the primary auditory cortices to the auditory stimulus. The adolescents with auditory-tag-driven signals in the left temporal cortex were older than those who did not show responses. Visual cortices showed enhanced visual-tag-related activity with attention, but there was no cross-modal effect, perhaps due to the developmental effect observed in the temporal areas. The visual-tag-related responses in the occipital cortex were enhanced in the higher PA group, irrespective of task demands. In summary, sensory cortices are unequally involved in cross-modal attention in the adolescent brain. This involvement seems to be enhanced by attention. Higher PA seems to be associated with a specific visual engagement benefit in the adolescent brain.