The film was inspired by the 1999 book The Coming Global Superstorm by Art Bell and Whitley Strieber, and Strieber himself wrote the film's novelization.

Roland Emmerich wrote a first draft of the script and showed it to producer Mark Gordon, who had previously produced Emmerich's film The Patriot; Jeffrey Nachmanoff then came in to help with rewrites.

On May 1, 2002, CAA held an auction sending the script to all major studios with a term sheet indicating a $125 million budget, including $10 million for Emmerich against 10% of the gross; Twentieth Century Fox closed the deal just two days later.

Filming took place predominantly in Montreal and Toronto, with additional footage shot in New York City and Chiyoda, Tokyo, running from November 7, 2002 to October 18, 2003.

For the destruction of New York, effects artists used a 13-block-sized, LIDAR-scanned 3D model of Manhattan built from over 50,000 scanned photographs, abandoning an initially considered miniature set.

The film's opening flyover of Antarctica was a fully CGI shot lasting about two and a half minutes, created by digitally scanning miniature iceberg models sculpted from styrofoam, and was at the time the longest continuous all-CGI shot in film history, surpassing the space zoom-out from Contact (1997).

The storm surge sequence was so complex that three different special effects vendors worked on it, with digital water created by either Digital Domain or the smaller effects house Tweak Films depending on the shot, while miniatures were used for an underwater scene showing a bus crushed by a drifted Russian tanker's bow.

The Japanese dub of the film features an exclusive theme song titled 'More Than a Million Miles', performed by a band coincidentally also named Day After Tomorrow.

Emmerich did not deny that the film's portrayal of a weak U.S. president and the physical resemblance of actor Kenneth Welsh's character to Vice President Dick Cheney were intended as criticism of the George W. Bush administration's climate change policy.

For twenty years the film held the record for the highest opening weekend for a natural disaster movie, until it was surpassed by Twisters in 2024.