The company says the change will apply to its original Capri Sun drinks, and that the number of calories will go down to 50 per pack, from 60.
The reformulated drinks started shipping to retailers this week and should start appearing on shelves nationally in coming weeks, the company said.
For its Roarin' Waters line, which is marketed as being low-calorie, the company is replacing the high-fructose corn syrup with sugar and the artificial sweetener sucralose with the zero-calorie sweetener stevia, extracted from a plant.
"Moms and dads tell us they want to feel good about what they give their children to eat and drink, and that they're increasingly interested in health and wellness," Kraft said in a statement.
High-fructose corn syrup has become a maligned ingredient in recent years, in part because it's seen as a cheaper, less-natural substitute for sugar.
In hopes of combating negative perceptions, the Corn Refiners Association in 2010 submitted an application to the Food and Drug Administration to have the sweetener renamed "corn sugar" on nutrition labels. The request was denied.
The industry group has also commissioned studies on perceptions of sweeteners and shared the results online. For instance, it notes that "67% of consumers agree that moderation is more important than specific sweetener types."