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As a carbohydrate meal is eaten and digested, blood glucose levels rise, and the pancreas secretes insulin. Glucose from the portal vein enters the liver cells (hepatocytes). Insulin acts on the hepatocytes to stimulate the action of several enzymes, including glycogen synthase. Glucose molecules are added to the chains of glycogen as long as both insulin and glucose remain plentiful. In this postprandial or "fed" state, the liver takes in more glucose from the blood than it releases.

After a meal has been digested and glucose levels begin to fall, insulin secretion is reduced, and glycogen synthesis stops. About four hours after a meal, glycogen begins to be broken down to be converted again to glucose. Glycogen phosphorylase is the primary enzyme of glycogen breakdown. For the next 8-12 hours, glucose derived from liver glycogen will be the primary source of blood glucose to be used by the rest of the body for fuel.

Glucagon is another hormone produced by the pancreas, which in many respects serves as a counter-signal to insulin. When the blood sugar begins to fall below normal, glucagon is secreted in increasing amounts. It stimulates glycogen breakdown into glucose even when insulin levels are abnormally high.

Glycogen in muscle and other cells

Muscle cell glycogen appears to function as an immediate reserve source of available glucose for muscle cells. Other cells that contain small amounts use it locally as well. Muscle cells lack the ability to pass glucose into the blood, so the glycogen they store internally is destined for internal use and is not shared with other cells, unlike liver cells.

Glycogen and marathon running

Due to the body's ability to hold no more than around 2,000 kcal of glycogen, marathon runners commonly experience a phenomenon referred to as "hitting the wall" around the 20 mile (32 km) point of a marathon.