Best-selling author Alistair MacLean wrote the novel and the screenplay of Where Eagles Dare at the same time. It was his first screenplay; both film and book became commercial successes.

The production, which hired some of the top moviemaking professionals of the period, is considered a classic of its genre. Major contributors included Yakima Canutt, the legendary Hollywood stuntman, who as second-unit director shot most of the action scenes, famed British stuntman Alf Joint who doubled for Burton in some of the most thrilling sequences such as the aerial fight on top of the cable car, award-winning conductor and composer Ron Goodwin who wrote the film score and future Oscar-nominee, Arthur Ibbetson who worked on its cinematography.

Burton approached producer Elliott Kastner for ideas, who consulted with MacLean. At that time, most of MacLean's novels had either been made into films, or were in the process of being filmed, nevertheless, Kastner persuaded MacLean to write a new story; six weeks later, MacLean delivered the script of Where Eagles Dare.

The title derives from Act I, Scene III in William Shakespeare's Richard III: "The world is grown so bad, that wrens make prey where eagles dare not perch".

However once filming began, Clint Eastwood and Richard Burton reportedly dubbed the film 'Where Doubles Dare' due to the amount of time stand-ins were used for the action sequences.

It is World War II, in the winter of 1943-44; U.S. Army Brigadier General George Carnaby, one of the chief planners of D-Day, is captured by the Germans when his aircraft is shot down en-route to Crete. He is taken to the Schloß Adler (The Castle of the Eagles – hence the story's title), a fortress high in the Alps that is the headquarters of the German Secret Service in southern Bavaria. A special team of mainly British commandos is hurriedly assembled and briefed by Colonel Wyatt Turner and Admiral Rolland of MI6, and led by Major John Smith and US Army Ranger Lieutenant Morris Schaffer. Their mission is to parachute into enemy territory, infiltrate the Schloß Adler, and rescue General Carnaby before the Germans can interrogate him. Agent Mary Elison, an MI6 operative, accompanies the mission in secret.

As the mission begins, two members of the team are mysteriously killed, but Major Smith is unperturbed and keeps Lt. Schaffer as a close ally. Contriving to get the entire party captured, Smith and Schaffer, being officers, are separated from Thomas, Christiansen, and Berkeley, the only three remaining NCOs of the group. Smith and Schaffer kill their captors, and blow up a supply depot before hitching a ride atop a cable car - the only safe approach to the castle. Mary, posing as a new maid, was brought into the castle earlier by Heidi, an MI6 agent disguised as a barmaid in the nearby village, and Major von Hapen, a Gestapo officer and Heidi's acquaintance, who becomes infatuated with her. After settling, Mary allows Schaffer and Smith to climb in through an open window overlooking the castle's station.

General Carnaby's interrogation is already underway, carried out by officers Gen. Rosemeyer and Col. Kramer, where Thomas et al. have arrived and revealed themselves to be German double agents. Smith and Schaffer intrude, but Smith suddenly betrays and disarms Schaffer, and establishes himself as "Major Johann Schmidt" of SS Military Intelligence. He then exposes the true identity of Carnaby - that of a U.S. Army Corporal named Cartwright Jones, posing as the real General, and also explains that Thomas et al. are actually British impostors. To test them, Smith proposes that they write the names of their fellow conspirators to be compared to the personal list in his pocket, and divulges the name of Germany's top agent in Britain secretly to Kramer, who silently affirms it. After the three finish writing their lists, Smith reveals his list to Kramer, which appears to be blank. To the room's collective surprise, Smith admits that the rescue operation was actually a cover for the real mission - to discover the identities of German spies who have infiltrated Britain.

Meanwhile, Mary, preparing the explosives, meets von Hapen again; he takes her on a date to the castle's cafe, and subtly forces her to recite the tale of her assumed identity. He finds faults in her story, prompting him to do a private investigation; he happens upon the meeting just as Smith finishes his explanation, and becomes hostile. Mary's sudden entrance distracts von Hapen enough for Schaffer to quickly kill him and the other German officers, after which the remaining group make their escape. Thomas, Berkeley and Christiansen are taken prisoner. Schaffer sets explosives to create diversions around the compound and Smith leads the group to the radio room, where he informs Rolland of their success. They then battle their way to the cable car station; Thomas is sacrificed as a decoy, and Berkeley and Christiansen attempt their own escape, but Smith climbs atop the cable car they steal and destroys it with an explosive. Smith makes it back on a returning cable car and rides back down with the others, but the group abandons it mid-descent to reunite with Heidi and board a bus, prepared earlier as their escape vehicle. They drive hard to an airfield with soldiers in hot pursuit, and barely make it onto a disguised extraction plane, where Colonel Turner is waiting for them.

Smith briefs Turner on the mission, and also confirms a suspicion he and Rolland had shared since before the mission started - that Turner himself is the top Nazi agent in Britain, whose name the late Kramer had agreed to before; Turner had been lured into participating so MI6 could expose him, with Mary (Smith's trusted partner) and Schaffer (an American with no connection to MI6) specially assigned to the team to ensure the mission's success. Deciding to save face, Turner commits suicide by jumping out the plane, leaving the others to rest easily on the flight home.