The series was announced in October 2020 as part of a multi-year production deal between Jon Stewart and Apple, marking his return to current affairs television since leaving The Daily Show in 2015.

The show's title, The Problem with Jon Stewart, and a late 2021 premiere date were only revealed on April 7, 2021, months after the project itself was announced.

In early 2021 the production team was assembled, with network news veteran Brinda Adhikari hired as showrunner and executive producer, Chelsea Devantez as head writer, and Lorrie Baranek as Stewart's executive in production.

Filming began in front of a live studio audience in New York City on July 14, 2021.

Each hour-long episode was designed to focus on a single issue tied to the national conversation and to Stewart's personal advocacy work, and every season was accompanied by a companion podcast co-hosted by Stewart and his writing and production staff.

The series was cancelled in October 2023 after two seasons due to creative differences between Stewart and Apple, reportedly involving disagreements over covering artificial intelligence, Israel, and China.

In an April 2024 interview with FTC Chair Lina Khan on The Daily Show, Stewart revealed that Apple had asked him not to have Khan on the show, allegedly saying 'please don't talk to her,' and that Apple also would not let him discuss AI in the same episode.