Rats are suitable animal models in which to study the effects of gastric bypass surgery. However, construction of gastrojejunal anastomosis in the rat is technically demanding and is associated with high rate of postoperative complications. The aim of this study was to explore the feasibility and efficacy of the magnetic compression technique (MCT) in side-to-side gastrojejunal anastomosis in rats. Thirty male rats underwent gastrojejunal anastomosis using one of three techniques: hand-sewn, magnetic compression using cuboid magnets, and magnetic compression using magnetic rings. The mean anastomosis time using the magnetic compression technique was significantly less than that of the hand-sewn technique (3.6 ± 0.96 and 6.50 ± 1.58 vs. 14.40 ± 2.37 minutes,). The survival rate was highest in animals treated with magnetic compression using cuboid magnets (100%), followed by animals treated with magnetic compression using magnetic rings (90%) and then hand sewing (70%). The mean burst pressure did not differ significantly between the magnetic compression and hand-sewn anastomoses. Anastomoses constructed by magnetic compression were smoother and flatter than hand-sewn anastomoses. The results showed that MCT is a simple and feasible method for gastrojejunal anastomosis in the rat.