The show's standard opening sequence interplays images of the glyph symbols alongside words representing fringe science topics, such as "teleportation" and "dark matter". Within the third season, with episodes that took place primarily in the parallel universe, a new set of titles was used, following a similar format, though tinted red instead of blue and using alternate fringe science concepts like "hypnosis" and "neuroscience". The difference in color has led some fans to call the prime universe the Blue one in contrast to the parallel Red one. In the third-season episode "Entrada", the titles used a mix of both the blue- and red-tinted versions, given that the episode took place equally in each universe. In the two flashback episodes, "Peter" and "Subject 13," a variation on the sequence, using retro graphics akin to 1980s Technology and phrases like "personal computing" and "genetic engineering," was used. For the dystopian Future third-season episode "The Day We Died," a black-toned theme, with more dire phrases like "hope" and "water," was used. The fourth-season premiere, "Neither Here Nor There" introduced an amber-toned title sequence with additional new terms that is used for nearly all fourth-season episodes. The fourth-season episode "Letters of Transit," which returned to the Future dystopian universe, and the subsequent fifth-season episodes, feature a cold-toned title sequence with phrases such as "joy," "private thought," "free will," and "freedom," ideas which have been lost in this Future. There is one frame in the opening sequence in which the words "Observers are here" flash very quickly, and the opening sequence must be paused to see them.

Season 4 begins in an alternate timeline, one in which September had failed to save the alternate version of Peter in 1985, according to the Observers. This creates a butterfly effect influencing the main characters' pasts but otherwise stabilizing both universes due to the creation of the bridge. Peter is pulled into this new timeline due to the actions of the alternate timeline's Fringe team, which includes Lincoln Lee (Seth Gabel). Peter initially works to return to his own timeline, fueled by fears that his memories are altering Cortexiphan-dosed Olivia's of this timeline, but after encountering a wounded September, Peter comes to learn that this timeline is truly his home, and both he and Olivia come to accept the change, rekindling their affair. September also reveals to Peter that the Observers needed to erase Peter's son, Henry, to assure their Future will be created, though noting that Peter's Future child with Olivia will be important. Meanwhile, in the present, william Bell has instructed David Robert Jones, alive in this timeline, to work with the parallel universe's version of Nina Sharp to synchronize the two universes, aiming to collapse them both and pave the way for a third universe under Bell's control, using Olivia's Cortexiphan powers to enable the collapse. The Fringe division is forced to close the dimensional bridge, but this fails to stop Bell's plan. Walter is left with one choice, to shoot and kill Olivia, her death disrupting the process and saving the world. Olivia's "death" is only temporary, as the Cortexiphan in her body is consumed to repair the bullet wound, leaving her alive and healthy but lacking her psionic abilities. As Olivia and Peter begin their lives together, September appears to Walter and warns that the Observers "are coming".

After developing the core concepts of the show, Abrams began to seek studios to develop the show; Abrams' past successes led to Warner Bros. Television and the Fox Television Network to quickly jump on board the project. Peter Roth, the chief executive of Warner Bros. Television, had been actively seeking to bring any Abrams' project to his studio, and heard Abrams' pitch for Fringe at a dinner meeting in August 2007. Similarly, Kevin Reilly, the entertainment chairman at Fox, knew that it was critical for him to bring the next Abrams' project to his network, and worked with Roth to assure this would happen.

On August 27, 2008, a prequel comic book (leading right up to the moment in the pilot where Olivia 'first' meets Walter) written by Zack Whedon was released by DC Comics under its WildStorm imprint. This was to be the first issue of a monthly 6-issue limited series but the others were delayed until January 2009, when monthly publication resumed, with the sixth and final issue scheduled for release on June 17. The Vice President of WildStorm, Hank Kanalz, explained the publication hiatus: "The Writers of the show want to make sure the comic book is integrated into the mythology of the Fringe world, so we have decided to refocus the direction of the comic book. Unfortunately, this means that we will have some delays, but will be back in January."

The first season of Fringe was released on DVD and Blu-ray Disc on September 8, 2009 in region 1. In addition to all the episodes that had been aired, extras include three commentary tracks, unaired scenes, gag reels and behind the scenes features. A "Fringe Pattern Analysis" feature is included on the Blu-ray version as an exclusive. The sets were released on September 28, 2009 in region 2 and on September 30, 2009 in region 4.

On June 23, 2010, the first issue of Tales From the Fringe, the second six-part monthly series, was released, while the final issue was released on November 24, 2010.

Additionally, in September 2011, DC released the first issue of Beyond the Fringe comic series. With the first story written by Joshua Jackson titled "Peter and the Machine". The comic issues will alternate with an 'A' story and a 'B' story each. For Example, "Peter and the Machine" will take place in issues one, three, and so on until the story is finished and a new 'A' story starts up.

At San Diego Comic-Con 2012, actor John Noble mentioned that a film could be made further down the line.

The fifth season includes featurettes titled "A Farewell to Fringe" and "Fringe Panel at Comic-Con 2012", as well audio commentaries and a gag reel. It was released on Blu-ray and DVD on May 7, 2013 in region 1 and on May 13, 2013 in region 2. A complete series box set was also released on the same dates of the fifth season release in the respective regions.

An encyclopedia guide, September's Notebook — The Bishop Paradox, written by Tara Bennett and Paul Terry who had previously written the Lost Encyclopedia for Lost, was released in March 2013. A three-part series of prequel novels written by Christa Faust was released throughout 2013 and 2014. Each novel deals with a member of the Fringe team's past. The first is titled The Zodiac Paradox and is about Walter and his discovery of Cortexiphan. The second in the series is titled The Burning Man and is based on Olivia and how she was first exposed to Cortexiphan. The third is titled Sins of the Father and is about Peter's life in 2008 just before the point of time when the series starts.

In 2015, Bustle declared "White Tulip" as "one of the greatest hours in television history". He wrote, "'White Tulip' is an hour of television that shouldn't work, that technically doesn't even exist... but thank god it does, because it's one of the most powerful episodes ever created — and it showcases why Fringe is one of the most criminally underrated series of our time."