After completing The Hunt for Red October, John McTiernan wanted to direct Clear and Present Danger but left the production after an early script by John Milius was rejected in favor of adapting Patriot Games first.

Milius's first draft was more faithful to the original novel than the final film, and he later added the sequence in which Jack Ryan is ambushed in SUVs; he also revealed the original ending had Cortez traveling to Washington to kill the National Security Advisor before being killed in a mugging by drug addicts.

Tom Clancy was reluctant to allow further adaptations of his work after being dissatisfied with Patriot Games, and only agreed to Clear and Present Danger after negotiations with Paramount Pictures and a large financial deal.

Donald E. Stewart was hired in March 1992 to rewrite Milius's script to give Jack Ryan more screen time, and after Clancy criticized that draft, Steven Zaillian rewrote it again to try to win his approval, while Milius stayed on as a consultant for the action scenes.

The Pentagon objected to the script's negative portrayal of the U.S. President, the national security advisor, illegal covert U.S. military operations in Colombia, and the depiction of Colombia, requiring rewrites to secure approval for military equipment use.

The film was shot in Mexico instead of Colombia because filming on location there was deemed too dangerous, with Mexico City standing in for Bogotá and the Hacienda San Gabriel de la Palmas in Cuernavaca used as Escobedo's headquarters.

Production in Mexico was further complicated by the outbreak of the Chiapas conflict, and the shoot ran significantly behind schedule and over budget.

Some footage shot in the United States was destroyed by the 1994 Northridge earthquake, and after poor test screening results, parts of the film were reshot using new scenes written by Stewart and Zaillian.

The film's score was composed by James Horner, with an album featuring selections from it released by Milan Records on August 2, 1994.