A few of Banjo-Tooie's worlds were originally planned for its predecessor, Banjo-Kazooie, such as the fire side of Hailfire Peaks and Glitter Gulch Mine. Many of these were cut primarily because of time constraints.

Gobi mentions leaving for the "Lava World" in Click Clock Woods, which adds up as Gregg Mayles' concept art for the cut lava world shows that Gobi would have been present. Gobi would eventually live up to his promise by appearing in the fire side of Hailfire Peaks in Banjo-Tooie, after being freed in Witchyworld.

According to two interviews with Famitsu in 1998, Shigeru Miyamoto cited Rare's exceptional graphical and technical work on Banjo-Kazooie as a factor for why The Legend of Zelda: Ocarina of Time was delayed, as Miyamoto and his team felt they needed to compete with it. He thought a 3D action platformer of its kind running that well on Nintendo 64 hardware was "so amazing that we don't want to be outdone", and "if Mario's a makunouchi bento, Banjo's a deluxe makunouchi bento." Some reviews of Ocarina of Time at its release compared its graphics, frame rate and textures with Banjo-Kazooie's, and felt Ocarina of Time did not perform as well in that field.

In the Japanese version of Super Smash Bros. Ultimate, Banjo & Kazooie's down special, Rear Egg, is called おケツタマゴ (Oketsu Tamago), which in English directly translates to "Ass Egg". This particular name was utilized for the Japanese localization of Banjo-Kazooie, at least its Japanese website.

It's worth pointing out that, in the English version of Banjo-Kazooie and Banjo-Tooie, this move has no name, as it's rolled into Egg Firing as one ability. However, internally in both games, the animation is indeed named "egg ass", which the Japanese version literally translates for its name.

Tiptup is a recurring NPC character in the Banjo-Kazooie series that, along with Banjo, also made his debut in Diddy Kong Racing in 1997. However, Tiptup was originally the name of a turtle in Dream: Land of Giants, the game that would eventually morph into Banjo-Kazooie. Halfway through the development of BK, the development team behind Diddy Kong Racing (or Pro-Am 64 as it was called before Diddy Kong was included later on) were in need of names for their racers, one of which happened to be a turtle, and thus it was given the Tiptup name. Tiptup was then incorporated into future Rare games like Banjo-Kazooie and Banjo-Tooie.

In Super Smash Bros. Ultimate, when Banjo & Kazooie either run with the Talon Trot or uses their down special Grenade Egg, a flap on the bottom of Banjo’s backpack opens up to use said move. According to Steve Mayles (the original character designer for Banjo & Kazooie) on Twitter, this is a concept that he wanted to initially use in the original Banjo-Kazooie, but limitations of the Nintendo 64 prevented it.

Inside the game's files is an unused song called "Mumbo's Rain Dance.".

There's an unused underwater variation of the Freezeezy Peak theme which cannot be heard in-game as the water in that level is too cold (and too shallow) to swim in. Even if the player travels through the icy water submerged after having been turned into a walrus by Mumbo, the music still won't change.

Before Rare decided to use Banjo to replace the character Edison (the main character of the canceled Project Dream project that would later become Banjo-Kazooie), they wanted the main character to be a rabbit.

An early idea for the game was to replace a majority of the dialogue in the game with "Bubblespeak". Thought bubbles would appear above the character's heads featuring an image inside, either still or moving, conveying any advice, warning or info that they're trying to tell. This was to make the dialogue in the game more uni-lingual and funnier.

In an early development version of Mad Monster Mansion, there was a painting in the dining room of the windmill from Twelve Tales: Conker 64 - The game that would later become Conker's Bad Fur Day.

Inside the game's data is an unused sign that says "On Vacation" It was most likely originally intended to be used for Mumbo's hut in the Winter area of Click Clock Wood. Instead, a Beehive tells Banjo that Mumbo is on vacation.

The original sound for collecting an Egg changed in development. It's not know why it was scrapped, but it might have been because the sound became rather annoying when collecting large amounts of eggs.

There is a unused test map in the game's data. It consists of 8 slopes arranged in a circle formation. This test map was most likely made to test Banjo's climbing ability.

The music for Gruntilda's Lair strongly resembles an old song called "Teddy Bear's Picnic". The composer, Grant Kirkhope, has acknowledged that he probably was thinking of Teddy Bear's Picnic when he wrote Gruntilda's Lair, but doesn't remember it being a conscious decision.

Inside Banjo's house is a portrait of Banjo & Kazooie walking through a forest. While commonly believed to be an early screenshot of the level Fungi Forest which would later appear in Donkey Kong 64, this is actually a screenshot from an early build of Banjo-Kazooie's prototype Dream: Land of Giants, after the original protagonist was replaced by Banjo.

In an early E3 video, it shows that Banjo and Kazooie could fly at any time they wanted without the use of a flight pad. This was most likely removed to limit the amount of area the player could cover at one time.

A poster featuring an early design of Berri from Conker's Twelve Tales can be found in Rusty Bucket Bay. This would be replaced by a poster of Conker from from the game it would be reworked into in the Xbox Live Arcade version.

An image of Donkey Kong appeared in an early build, but was replaced with an image of Banjo's sister, Tooty.

Grant Kirkhope, the composer of the game, provided the voice of the pots in Mad Monster Mansion that say "Thank You" when the player deposits an egg in them. According to Kirkhope, he had to redo the line several times because Nintendo thought he was saying "Fuck You".

There's an unused firefly sprite which appears similar to the Beehive's Bee sprite which even uses the same wings. It's possible this was intended to be used for the world Mad Monster Mansion, the only level set during night.