- In "Order Up!", an ender pearl can be seen on display inside the Order Hall.
- In "A Portal to Mystery", 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 "Access Denied", Jesse and Ivor use the remaining two ender pearls from the White Pumpkin's lair to teleport off the cliff when they are surrounded by Mind Controlled Citizens in Crown Mesa.
- In Minecraft, endermen have a chance to drop an ender pearl when killed. The White Pumpkin most likely 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 five, 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".