Laparoscopic fundoplication is the current surgical gold standard for the treatment of refractory gastroesophageal reflux disease (GERD). Magnetic sphincter augmentation (MSA) is a less invasive, standardized, and reversible option to restore competency of the lower esophageal sphincter. A comparative cohort study was conducted at a tertiary-care referral center on patients with typical GERD symptoms treated with systematic crural repair combined with Toupet fundoplication or MSA. Primary study outcome was decrease of Gastroesophageal Reflux Disease-Health Related Quality of Life (GERD-HRQL) score. Between January 2014 and December 2021, a total of 199 patients (60.3% female, median [Q1-Q3] age: 51.0 [40.0-61.0]) underwent MSA (n = 130) or Toupet fundoplication (n = 69). Operative time and hospital stay were significantly shorter in MSA patients (P< 0.0001). At a median follow-up of 12.0 [12.0-24.0] months, there was a statistically significant decrease of GERD-HRQL score in both patient groups (P= 0.001). The mean delta values did not significantly differ between groups (P= 0.7373). The incidence of severe gas bloating symptoms was similar in the two groups (P= 0.7604), but the rate of persistent postoperative dysphagia was greater in MSA patients (P= 0.0009). Six (8.7%) patients in the Toupet group had recurrent hiatal hernia requiring revisional surgery in one (1.4%). In the MSA group, eight (7.9%) patients necessitated through-the-scope balloon dilation for relief of dysphagia, and six patients had the device removed (4.6%) because of persistent dysphagia (n = 3), device disconnection (n = 1), persistent reflux (n = 1) or need of magnetic resonance (n = 1). Toupet and MSA procedures provide similar clinical outcomes, but MSA is associated with a greater risk of reoperation. Randomized clinical trials comparing fundoplication and MSA are eagerly awaited.