The game play consists of a red button, which can be switched in size, with a chicken on it. When the button is pressed, the chickens are released and therefore earn money for the eggs they produce. This money can be used to further upgrade the egg farm through lab research, thus increasing the value of the eggs, the production rate and the size of the player's distribution fleet. To increase the farm's profitability, players can build larger spaces (called coops) to raise more chickens, buy larger trucks to transport more eggs and more granaries, and keep the farm running longer on its own. There is also Epic Research, which is purchased with Golden Eggs and is permanent (it does not reset when the player upgrades Golden Eggs or Reputation). This includes lowering the price of buildings, increasing soul egg boosts, and researching and increasing the size of hatcheries.

The Egg Company also allows players to earn currency by watching advertising videos. Every few minutes, a white truck will pass by and drop off a package with money (which increases in value as the farm increases in value). As the player's farm earns more and produces more, the player can upgrade to a different egg and start over, but each egg will sell for a higher price. Later egg types, trucks and chicken coops have a futuristic theme. There are also drones that give the player cash when clicked.

Sometimes, players may get some golden eggs. Golden eggs are premium currency; they can be obtained in-game or purchased with real money and do not reset when upgrading eggs or restarting. Using said currency, players can buy temporary props such as clicking on unlimited chickens for ten minutes or double earnings for two hours, or can get epic research to upgrade other areas such as getting rare (elite) drones, or increasing the time of double earnings. When a player's farm reaches a certain value based on eggs, the player can upgrade the type of eggs sold on the farm to higher value eggs and start over.