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The idea for the Bundle was from Jeff Rosen of Wolfire Games. Rosen describes the inspiration coming to him through similar sales of bundle packages on the Steam platform. Rosen had noted that such sales would have viral word-of-mouth spread across the Internet. Influence also came from a previous "pay-what-you-want" sale for World of Goo upon the title's first anniversary; over 57,000 copies of the game were purchased during this sale, generating over US$117,000 after considering PayPal handling fees. Rosen by this point was well connected with other independent developers; for example his brother David is listed as being a game tester for the Penumbra series, and Penumbra's composer Mikko Tarmia contributed to Wolfire Games' game project Overgrowth. Wolfire had also recently teamed with Unknown Worlds Entertainment to offer a bundle based on their Natural Selection 2 game. The porter of Lugaru to Linux was Ryan C. Gordon, who was also responsible for porting Aquaria to Linux. With his close ties to these independent developers, as well as Ron Carmel of 2D Boy, Rosen was able to assemble the package, taking advantage of merchant sales systems offered by PayPal, Amazon Payments, and Google Checkout to minimize the cost of transactions and distribution. The site later added the option to pay via Bitcoin only through Coinbase. As of 2025, the option to pay by BitCoin is no longer supported.

Though achieving word of mouth was a key element of the potential success of the bundle, Rosen also recognized that the process to purchase the Bundles had to be simple; including elements like user account registration or the use of a secondary download client would have potentially driven away sales. Rosen also sought to include charities in the bundle, allowing the purchaser to choose how to distribute the funds between the developers and charities. Rosen believed Child's Play was a worthwhile cause that brought video games to hospitalized children and helped to fight the stigma of video games, while he selected the Electronic Frontier Foundation to support their anti-DRM stance. The means of "pay-what-you-want" would allow purchasers to simply give the money to the charities, but Rosen felt this was not an issue and would "consider that a success" of the sale. Rosen and Wolfire employee John Graham provided technical support during the sales, handling thousands of requests through a few all-night email and chat sessions.

Rosen and Graham began planning for a second Humble Indie Bundle, which launched in December 2010 and raised $1.8 million. The two recognized the value proposition of continuing this model and spun out Humble Bundle as its own company shortly after the release of the second bundle. Rosen and Graham served as its founders. Sequoia Capital had invested $4.7 million of venture capital into Humble Bundle by April 2011, allowing Rosen and Graham to hire staff to help curate further bundles and handle customer services.

On October 13, 2017, Humble Bundle announced it had been acquired by IGN Entertainment, a subsidiary of Ziff Davis. According to the company, Humble Bundle was to continue to operate as a separate entity within IGN, with no plans to change its current business approach in the short term. Instead, Graham cited "a lot of opportunities" for the customer bases of both companies. He said that the acquisition by IGN enables them to continue to do the same sales and charity promotions "faster and better" with IGN's resources backing them. IGN's executive vice president Mitch Galbraith said that they felt Humble Bundle was a "great fit" for IGN, and would also help IGN to "give something back" by supporting its charitable driv