An 89-year-old woman who was bedridden suffered repeated vomiting due to superior mesenteric artery syndrome (SMAS). We performed gastrojejunostomy via the magnetic compression anastomosis (MCA) technique because her situation was not improved by conservative therapy and because the operative risk was high. We prepared two neodymium magnets: a flat plate-shaped magnet (15 × 3 mm) and a ring-shaped magnet of the same size. The ring-shaped magnet which passed through a guidewire was pushed to the duodenum by an endoscope over the guidewire. The duodenal stricture was balloon-dilated in front of the magnet, and the magnet was pushed all together beyond the stricture and placed at the duodenojejunal junction. Subsequently, the flat plate-shaped magnet was delivered endoscopically to the stomach using a biopsy forceps. The magnets were attracted towards each other transmurally after one more flat plate-shaped magnet was added to the gastric-side magnet. Completion of gastrojejunostomy was confirmed while retrieving the magnets 10 days after starting compression. She has been asymptomatic for 1 month since anastomosis. Endoscopic gastrojejunostomy using MCA was an effective, low-invasive treatment for SMAS.