The game's development started with the creation of the characters and watching system. The main designer and the other creative designers were initially unsure of which direction the game should take; months had been spent selecting a camera view and layout that would be appropriate. The original concept involved the game having fixed path much like a different sort of game, before the choice was developed to decide on a free-roaming 3D design. Although the majority of Super Mario 64 would end up featuring the free-roaming design, elements of the original fixed path concept would remain in certain parts of the game, particularly in the three Bowser encounters. One particular of the programmers of Super Mario 64, Giles Goddard, explained that these few linear elements survived as a method to force players into Bowser's lair rather than to encourage exploration.

The development team placed high priority on getting Mario's movements right, and before levels were created, the group was testing and refining Mario's animations on a simple grid. The first test scenario used to test out controls and physics involved Mario and a golden rabbit named "MIPS" by the developers, the latter of which was included in the final release of the game as a means to obtain two of the Power Stars. The developers initially tried to make the game split screen co-op utilizing both Mario and brother. Initially, both the characters would start at different points within the castle and work their way through the game together. Nonetheless, developers were not able to make the gameplay function.

Some courses include specific cap power-ups that augment Mario's abilities. The Wing Cap permits Mario in order to fly; the Metal Cap makes him or her immune to almost all damage, allows him to resist wind, stroll underwater, and be unaffected through noxious gases; and the Vanish Cap renders him somewhat immaterial and allows him to walk via some obstacles such as wire mesh, along with granting invulnerability with a forms of damage.

The music had been composed by a professional musician, who used new interpretations of the familiar melodies from earlier games along with entirely brand new material. Super Mario 64 was among the first games in the series to function the little guy as the voice of Mario. It also features the actual voices of Princess Mango, who also wrote the actual English text for the game, and Isaac Marshall as Bowser. The characters speak more in the English version than in the Japanese version. In addition, dialogue and some sounds differ between your Japanese and English versions. Some of these vocal changes for the English release were brought to the Japanese save edition. When Super Mario 64 DS was launched, all the voices were stored consistent in both the British and Japanese versions.

Critics credit the initial success of the Nintendo 64 console to Super Mario 64. Edge magazine referred to it as being the Nintendo 64's "key launch title". Game Informer commented that the game helped the launch of the Nintendo 64 magazine and GameDaily also credited a lot of the initial enthusiasm of the Nintendo 64 system to the release of Super Mario 64.