Controlled navigation promotes full utilization of capsule endoscopy for reliable real-time diagnosis in the gastrointestinal (GI) tract, but intermittent natural peristalsis can disturb the navigational control, destabilize the capsule and take it out of levitation. A real-size magnetic navigation system that can handle peristaltic forces of up to 1.5 N was designed utilizing the computer-aided design (CAD) system Maxwell 3D (Ansoft, Pittsburg, PA), and was verified using a small-size physical experimental setup. The proposed system contains a pair of 50-cm in diameter, 10,000-turns copper electromagnets with a 10-cm by 10-cm ferrous core driven by currents of up to 300 Amperes and can successfully maintain position control over the levitating capsule during peristalsis. The addition of Bismuth diamagnetic casing for stabilizing the levitating capsule was also studied.