The purpose of this study was to investigate the effects of high-frequency repetitive Transcranial Magnetic Stimulation (rTMS) and aerobic exercises (AE) in addition to the pharmacological therapy (PT) in Alzheimer’s Disease (AD). Twenty-seven patients with AD aged ≥ 60 years were included in the study and divided into 3 groups (rTMS, AE and control). All groups received PT. rTMS group (n = 10) received 20 Hz rTMS over dorsolateral prefrontal cortex (dlPFC) bilaterally and AE group (n = 9) received the structured moderate-intensity AE for 5 consecutive days/week over 2 weeks. Control group (n = 8) only received PT. Cognition, balance, mobility, quality of life (QoL), and resting state functional brain activity were evaluated one week before and one week after the interventions. (ClinicalTrials.gov ID:NCT05102045). Significant improvements were found in executive functions, behavior, and QoL in the rTMS group, in balance and mobility in the AE group, and in the visual memory and behavior in the control group (p < 0.05). Significant differences were found in the behavior in favor of the rTMS group, and balance in favor of the AE group (p < 0.05). There was a significant increase in activation on middle temporal gyrus, intra calcarine, central opercular cortex, superior parietal lobule, and paracingulate cortex in Default Mode Network (DMN) in the rTMS group (p < 0.05). High-frequency rTMS over bilateral dlPFC may improve executive functions and behavior and lead to increased activation in DMN, structured moderate-intensity AE may improve balance and mobility, and PT may improve memory and behaviour compared to pretreatment in AD.