Cow Hunter is a point-and-click shooting game similar to many traditional hunting games with a supposedly humorous twist. Instead of targeting deer, players shoot cows, which in most cases are flying through the air. The game features several modes where players can use weapons such as the Cowabunga Rifle. The modes are as follows:

Skeet Shooting: Cows fly across the screen and the player shoots them. Bonus items such as hamburgers also appear. This mode includes three different locations. Players point and click to shoot the flying cows.

Cow Tipping: The player controls a disembodied hand used to tip over sleeping cows. Some cows are not yet asleep and will fire dung at the player. This dung must be clicked on to stop it.

Target Practice: Cows briefly pop their heads out from behind haystacks or around barn doors. The player must point and click to shoot them.