Protonix, or Pantoprazole is a proton pump inhibitor. This means that it is active at the mitochondrial level, preventing the movement of protons across the inner membrane which ultimately results in reduced production of ATP. ATP is a major source of energy for the cell, and therefore the body as a whole. Reduced levels of ATP can cause discomfort, which in your case (as well as others who take the drug) leads to specific side effects such as headaches.