Iris was based on the general concept of the 1999 film Shiri, and Shiri's director Kang Je-gyu was initially involved in developing the project for television before Kim Kyu-tae and Yang Yun-ho took over as directors.

Production began without the backing of a Korean broadcaster, as the production company deliberately tried to spark a bidding war among potential broadcasters before KBS was secured.

Son Ye-jin was considered for the female lead role but turned it down due to scheduling conflicts with other projects, leading to Kim Tae-hee being cast instead.

Lee Byung-hun's casting marked his first television role in five years after focusing on film work, including 2009's G.I. Joe: The Rise of Cobra, which was still filming when his casting was announced.

Lee Byung-hun's salary of 100 million won (about $90,000) per episode was the third highest in Korean drama history and six times the industry guideline rate, reportedly justified by his drawing power for Japanese investors.

The first scenes were filmed in Akita, Japan in March 2009, and Lee Byung-hun's popularity there caused thousands of fans to greet him at the airport, sparking a wave of Korean tourism to the prefecture.

Actors often performed their own stunts, including Lee Byung-hun jumping from the 130-meter-tall Tamagawa Dam in Semboku, Akita; Kim Tae-hee and other cast members underwent special training to prepare for the demanding action sequences.

On November 29, 2009, the production filmed a large-scale gunfight scene at Gwanghwamun Plaza and Sejong-ro in Seoul, closing five traffic lanes for twelve hours—the first time a Korean drama was allowed to film there, though it sparked controversy over unequal treatment compared to banned protests.

With a budget exceeding 40 billion won (about $35 million), Iris and its spin-off Athena: Goddess of War share the record for most expensive Korean dramas ever produced.

TBS purchased Japanese distribution rights for a record 400 million yen (about $4.2 million) and aired a Japanese-dubbed version in primetime, a first for a Korean drama in Japan, with actor Tatsuya Fujiwara voicing Kim Hyun-jun.

Two live stage show events in Japan in May 2010, combining cast interviews, scene re-enactments, and musical performances, drew sold-out crowds totaling over 60,000 attendees.

The popularity of the series revitalized nearly-decommissioned flights between Seoul and Akita due to a surge in tourist interest generated by the show's filming locations.

The Kia K7 sedan, designed by Peter Schreyer, made its first public appearance on television through this drama before its official commercial launch on November 24, 2009, during the show's original run.