In the Virtual Console release of the game, Jynx's sprite is altered to change her skin color from black to purple, keeping in line with the character's redesign since the international releases of Pokémon Gold & Silver in 2000, which was implemented following complaints from African-American writer Carole Boston Weatherford that the original design was evocative of blackface imagery.

While Game Boy and Game Boy Color sprites only allow for a maximum of three colors, the game's in-battle assets are composed of multiple 8x8 sprites composited together. Thus, the Virtual Console release was able to recolor Jynx's skin by only altering some of these tiles to replace black with purple. As no other Pokémon use this method, this makes Jynx's altered design the highest-detail Pokémon in any version of the Generation I games.

It is normally required to use HM05 to teach a Pokemon the move Flash which can then be used to light up dark caves. However, if Pikachu learns either Thunderbolt or Thunder, talking to it will cause it to spark and briefly light up the cave. While this technique does not keep dark caves lit until you exit them like Flash, it can be used repeatedly to traverse dark caves anyways.

If the player attempts to enter the Safari Zone without sufficient money to enter enough times, the worker who lets you in will take pity and allow you to enter with one Safari Ball. This was not an interaction in Pokemon Red & Blue and exists as a way to prevent the player from progressing in the game as a result of being unable to acquire enough money to get HM03 Surf, which is found in the park.

Among the NPC Pokémon trades in the game's data are three trades not assigned to any NPC, and thus inaccessible. One of them, a Beedrill in exchange for a Butterfree, exists in the data of every first-generation title. The nickname of the Beedrill even changed from version to version, but the trade remained unused.

Pokémon Yellow replaced two functioning trades with unused ones. One requests a Pidgeot for a Pidgeot, and the other is a Mew for a Mew. In Japan, both are nicknamed Matsumiya, presumably after Toshinobu Matsumiya, who was in charge of Yellow's scenario. In the English version, the Pidgeot is named MARTY and the Mew is named BART.

In Pokémon Yellow, The Youngster on Route 9 was inspired by the trainer A.J. from episode 8 of the Pokémon anime series. They both use a Sandshrew, speak of striving to win 100 battles in a row, and both Sandshrew know Fissure. In Pokemon Red/Blue, this trainer was originally named Jr. Trainer ♂, used a Growlithe and a Charmander, and never spoke of winning 100 battles.

In the Pikachu's Beach minigame, there is an unused 'Radness' bonus of 750 points coded into the game. There appears to be no way to achieve this without hacking.

Utilizing glitches, it's possible to teleport to the the Hall of Fame room directly at the beginning of the game, and beat the game in 0:00 (according to the game's internal clock) with a complete Pokedex. Depending on how the glitch is performed, it can be used to teleport to any location in the game.

There is a glitch in Pokemon Yellow where you can catch a level 1 Nidoking at the end of Viridian Forest, and level it up to level 100 with one fight. It involves catching a level 4 Caterpie and escaping from a trainer battle using an Escape Rope.

There is a piece of music in the game's code that is not in the final game. It's a song from a previous Game Freak game called Bushi Seiryuden Futari No Yusha and is used in the boss battle of the game.

The rival will eventually evolve his Eevee (and thus affect which other Pokemon are in his party) depending on the player's actions early in the game. If the player beats the rival at both Oak's Pokémon Research Laboratory and the early, optional, battle at Route 22, Eevee evolves into Jolteon. If the player loses one of these two battles, or passes up the Route 22 battle, Eevee evolves into Flareon. If the player loses at Oak's Lab, and loses or passes up the Route 22 battle, Eevee evolves into Vaporeon.

Data exists for a battle situation when the Trainer has no Pokémon, though it isn't actually used when entering a battle with no Pokémon in the final release. In this case, selecting any option other than Run shows the message "Hurry, get away!" This may have been a prototype for the initial battle with the wild Pikachu at the start of the player's adventure, as the player has no Pokémon at that point. It could also have been planned for a possible battle against a wild Spearow with Pikachu unable to battle, making it closer to the events of the anime.

Teaching Pikachu Surf from Pokemon Stadium will unlock a mini-game that can be played in Route 19 by talking to the Surfing Dude in the beach house.