An Ender Pearl can be seen on display inside the Order Hall.
The White Pumpkin uses Ender Pearls to escape Jesse. Jesse can also find five Ender Pearls in a Chest in the White Pumpkin's Lair, and will take five. Later, he/she uses three of them in his/her final confrontation with the White Pumpkin in the Portal Chamber.
- In Minecraft, Endermen have a chance to drop an Ender Pearl when killed. The White Pumpkin probably obtained them through this method.
- It is also possible that the White Pumpkin traded for Ender Pearls, as Endermen are known to be highly dangerous.
- In Episode 5, a spherical Ender Pearl can be seen on display inside the Order Hall.
- Spherical Ender Pearls do not exist in Minecraft, making it exclusive to Minecraft: Story Mode.
- In Minecraft, a player takes damage whenever they use an Ender Pearl. In Minecraft: Story Mode, no visible damage is taken, but Jesse complains multiple times throughout the game that teleporting with Ender Pearls is disorienting.