In Princess Toadstool's room in Mushroom Castle, looking behind the fireplace results in finding a mysterious item labeled "Toadstool's ???". It is never revealed what the item is, as finding it will result in either Toadstool's grandmother driving you away and giving you something else in exchange (the latter one being only on the first instance), or Toadstool angrily scolding you if you have her in your party. In the Japanese version, the item is labeled "Peach's XXX" (as Toadstool is called "Peach" in the Japanese version), giving less subtle ideas on what the item was originally intended to be. As a testament to being one of the Mario series' most famous dirty jokes, "Toadstool's ???" (now renamed to "Peach's" internationally) and the more risqué "Peach's XXX" would both be retained in the game's 2023 remake.

There is a secret code in the Japanese version of the original game. Going into the menu screen and entering Down, Up, Right, Left, Select, Start, Select, Start, B, will cause Toad to appear on-screen and say:


This code would be included internationally for the first time in the game's 2023 remake.

Various pop culture references that were made in the original English release of Super Mario RPG were removed in the remake:

• Mallow no longer mentions Bruce Lee prior to him and Mario going to fight Bowyer.
• Punchinello no longer references James Bond or the Thing during his boss fight.
• Mini Goomba's Thought Peek no longer references Theodore Roosevelt's aphorism "Speak softly and carry a big stick. You will go far."
• Stinger's Thought Peek no longer references the 1990 Madonna song "Vogue".
• The password clues on the Sunken Ship are no longer written by famous explorers.

Some of these references, such as the Bruce Lee reference, may be due to licensing issues.

High Boo's Thought Peek quote, "*sigh* ♪Stomp, stomp, clap. Stomp, stomp, clap.♪", references the 1977 song "We Will Rock You" by English glam rock band Queen. The song famously features a percussion section consisting of two stomped eighth notes followed by a clapped quarter note. Uniquely, this reference is a new addition to the remake; in the original SNES version, High Boo (known there as Li'l Boo) says "Beep pa doodle-dee!♪"

The Save Block has a different letter in the Dutch and Spanish translations. They have an "O" (opslaan) and a "G" (guardar) respectively, both meaning "to save". This is the same as in the Spanish translations of Paper Mario and Paper Mario: Sticker Star and in the Dutch and Spanish translations of Paper Mario: Color Splash and Paper Mario: The Origami King.