Objective Repetitive transcranial magnetic stimulation (rTMS), a non-invasive brain stimulation technique, offers a non-pharmacological therapeutic option for the management of Alzheimer's disease (AD). Studies have demonstrated that ferroptosis plays a pivotal role in the pathological onset and progression of AD, and the inhibition of neuronal ferroptosis can significantly ameliorate cognitive impairments associated with AD. The imbalance of calcium ion (Ca2+) homeostasis is intimately associated with the pathology of AD and serves as a catalyst for the induction of ferroptosis through various pathways. This study is designed to investigate whether rTMS can ameliorate Alzheimer's disease by inhibiting neuronal ferroptosis or maintaining calcium homeostasis, ultimately establishing a theoretical and experimental framework for the utilization of rTMS in AD treatment. Methods In the Methods section, APP/PS1 AD mice were subjected to both 0.5 Hz low-frequency and 20 Hz high-frequency rTMS treatments, and the efficacy of these treatments was evaluated using novel object recognition and Morris water maze tests. ELISA was employed to quantify the levels of glutathione (GSH), malondialdehyde (MDA), superoxide dismutase (SOD), Fe2+ within the hippocampi of mice from each group. HT-22 cells were induced to undergo ferroptosis via Erastin treatment, and subsequent to high- and low-frequency magnetic stimulation, cell viability was assessed using the CCK8 assay, while intracellular calcium ion concentration fluctuations were monitored using Fluo-4 AM. Results: The findings revealed that, when compared to normal mice, AD mice displayed a notable decline in cognitive function, accompanied by a substantial increase in ferroptosis levels and intracellular calcium ion concentrations. Both high-frequency and low-frequency applications of rTMS were found to significantly ameliorate cognitive impairments in AD mice, while also effectively mitigating the abnormal augmentation of neuronal ferroptosis and intracellular calcium ion levels. Conclusion: The present study underscores that both high-frequency and low-frequency repetitive transcranial magnetic stimulation (rTMS) exhibit efficacy in alleviating cognitive dysfunction in AD mice, potentially through the modulation of ferroptosis and intracellular calcium ion homeostasis.