Heat the oil in a deep fryer to 350 degrees F (175 degrees C).
Mix the flour, salt, and pepper in a large resealable plastic bag. Place cod in the bag, and gently shake to coat. Place eggs and crushed pretzels in two separate shallow dishes. Dip coated cod in the eggs, then in the crushed pretzels.
Fry coated fish 10 minutes in the preheated oil, turning once, until golden brown and easily flaked with a fork.
