Scott Miller founded the company in his parents' home in Garland, Texas, in 1987 as Apogee Software Productions to release his game Kingdom of Kroz.

In the late 1980s and early 1990s, the company popularized a distribution model where each game consists of three episodes, with the first given away free as shareware and the other two available for purchase.

In 2009, 3D Realms, citing financial issues, laid off its development team and the majority of its staff, effectively ceasing operations.

In the early 1980s, Scott Miller often spent time in the computer lab of the high school he was attending, programming text adventures on the facility's Apple II and getting to know fellow student George Broussard.

[1] Following graduation, both of them took jobs at local amusement arcade The Twilight Zone, allowing Miller to attend college and increase his interest in video games at the same time.

[1] At that time, he found a special interest in the Turbo Pascal programming language and its easy integration on IBM Personal Computers.

[1] The book fell into obscurity due to an oversaturated market but landed Miller a job as a video game critic for The Dallas Morning News and minor game-centric papers.

Miller acquired a 16.5k modem, which he installed in his parents' house in Garland, Texas, and started operating as a full-time independent game developer.

[1][3] The format appeared popular to him but ultimately proved unsuccessful when pitching them to publishers, adding to him not having a college degree or any professional experience in game development.

[1][2] Released on November 26, 1987, Kingdom of Kroz was the first game to bear the name of Miller's one-man company, Apogee Software Productions.

[12] On May 14, 2009, Take-Two, holders of the publishing rights of Duke Nukem Forever, filed a breach of contract suit against 3D Realms over failing to deliver the game.

[13] Take-Two Interactive asked for a restraining order and a preliminary injunction, to make 3D Realms keep the Duke Nukem Forever assets intact during proceedings.

Once [Duke Nukem Forever] comes out we'll be definitely looking to invest into other projects, and maybe other up-n-coming [sic] teams who are blazing new trails on smaller platforms, like smart phones and XBLA.

In February 2014, Gearbox sued 3D Realms, Interceptor Entertainment and Apogee Software, LLC for developing a new game called Duke Nukem: Mass Destruction.

[26] In May 2014, 3D Realms announced they were to publish Bombshell by Interceptor Entertainment,[27] and in October 2014 the company returned to distributing its own titles with a digital anthology collection.

On February 28, 2018, 3D Realms announced the game Ion Maiden, a prequel to Bombshell, developed by Voidpoint and using Ken Silverman's Build Engine.

In March 2023, 3D Realms announced that they hired Justin Burnham (formerly of Devolver Digital, Good Shepherd) to the position of CCO.

[42] On February 27, 3D Realms co-published (with Fulqrum Publishing) the Slipgate Ironworks and Killpixel Games-developed Wrath: Aeon of Ruin out of early access.