Background: Flat Magnetic Stimulation (FMS) is characterized by a stimulation generated by electromagnetic fields with a homogenous profile. One possible application is the treatment of stress urinary incontinence (SUI). We aimed to compare the objective, subjective, quality of life, and instrumental outcomes in women with SUI not eligible for surgery undergoing either FMS or pelvic floor muscle training (PFMT). Methods: This was a prospective interventional study. After proper counseling, patients with isolated SUI were divided according to their treatment of choice into FMS and PFMT groups. At baseline and after treatment, patients completed the International Consultation on Incontinence Questionnaire-Short Form, the Female Sexual Function Index, and the Incontinence Impact Questionnaire, and volumetric measurement of the urethral rhabdosphincter (RS) was performed. The Patient Global Impression of Improvement questionnaire and stress test defined subjective and objective cure rates, respectively. Results: We observed improvements in urinary-related quality of life scores and an increase in RS volume after FMS compared to baseline. All these outcomes were significantly better compared to women who underwent PFMT. Conclusion: Our study demonstrated that FMS is a safe and effective conservative option for SUI management in terms of objective and subjective cure rates.