High-altitude stress ulcer (HSU) has constantly been a formidable clinical challenge for high-altitude and severe hypoxia. Pulsed electromagnetic fields (PEMFs) have been verified to have the ability to penetrate tissues, and the biological effects have been confirmed effective on various tissue restorations. However, the therapeutic effect of PEMFs on HSU has been rarely reported. This study aimed to evaluate the effects of PEMFs on HSU healing systematically. Sprague-Dawley rats were assigned to control, HSU, and HSU+PEMF groups. The HSU models were induced by restraint stress under low-pressure hypoxia. The HSU+PEMF group was subjected to PEMF exposure. During the HSU healing, gastric juice pH values, ulcer index (UI), and histopathologic changes were investigated. Furthermore, tumor necrosis factor-α (TNF-α) was determined to analyze the severity of gastric membrane inflammations. Norepinephrine (NE), which influences gastric acid secretion, was measured. Results indicated the UI of the HSU+PEMF decreased faster than that of the HSU group. Histopathologic observation suggested that the ulcer tissue healing is faster in the HSU+PEMF group than in the HSU group. The TNF-α/total protein results revealed that the inflammation of the HSU+PEMF group is suppressed effectively. The pH values are higher in the HSU+PEMF group than in the HSU, as confirmed by NE examination. The results indicated that low-frequency PEMFs can penetrate stomach tissues to relieve the symptoms of HSU and promote the regeneration of disturbed tissues, thus implying the clinical potential of PEMF therapy for HSU treatment.