There might not be as many secret menu items at Papa John's as you may think. Papa John's pizza is, of course, a fast-food pizza chain, and as such, you can get most things on the regular menu changed if you want to add or subtract items from your pizza. With gluten free pizza, thin crust, and pan pizza, you can get pretty much whatever you want anyway. The pizza restaurant does have a few "secret" things, just like other restaurants like McDonald's, Starbucks, Chipotle, Dominos, Taco Bell, Burger King, and others do these days.
Papa John's Secret Menu Items
The only thing that's technically a secret item you can get that's not on the food menu at the "better ingredients, better pizza" chain is the Bacon Cheesesticks, according to SecretMenus.com. They're basically cheese sticks with some mozzarella cheese and bacon added.
The site reports that some locations actually do have the appetizer on the menu right alongside Papa John's favorites like pepperoni pizza, extra cheesy alfredo pizza, BBQ chicken wings, grilled buffalo chicken papadia, and desserts like the chocolate chip cookie and cinnamon pull-aparts. But if your local Papa John's doesn't have this item on the menu, they should have all the ingredients to make it, and it doesn't hurt to ask.
The outlet also noted that while the Cinnapie was a favorite at the restaurant, it was discontinued in 2016. There are copycat recipes out there so you can try, but it's not something Papa John's restaurants will really make for you anymore.
Although there are specific pizzas on the menu at Papa John's, you can pretty much add things like parmesan or grilled chicken, get more pizza sauce, or switch out the crust on most items, which sort of makes them "secret" options. But it makes it difficult to ask for anything all that "secret" from the Papa John's secret menu.
Just don't go asking for a Pizza Hut stuffed crust pizza at Papa John's if you don't want to be run out of the building!