The US aircraft manufacturer claims to have successfully tested the weapon on a one-hour flight during which it knocked out the computers of an entire military compound in the Utah desert.
It's thought the missile could penetrate the bunkers and caves believed to be hiding Iran's alleged nuclear facilities, the 'Daily Mail' reported.
However, experts have warned that the technology could be used to bring Western cities to their knees if it falls in the wrong hands.
During Boeing's experiment, the missile flew low over the Utah Test and Training Range, discharging electromagnetic pulses on to seven targets, permanently shutting down their electronics.
Boeing said that the test was so successful that even the camera recording it was disabled.
Codenamed the Counter-Electronics High Power Microwave Advanced Missile Project (CHAMP), it is the first time a missile with electromagnetic pulse capability has been tested.
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Boeing declined to release a film of the test, citing security reasons, but instead issued an artist's impression of it on video.
A stealth aircraft in the clip deploys a missile that emits radio waves from its undercarriage which knock out the computer systems inside the buildings below, the report said.
The company also released a real film showing a row of computers that can be seen shutting down when the electromagnetic pulse is switched on.
Experts believe the missile is equipped with an electromagnetic pulse cannon, which uses a super-powerful microwave oven to generate a concentrated beam of energy which causes voltage surges in electronic equipment, rendering them useless before surge protectors have the chance to react.
Keith Coleman, CHAMP programme manager for Boeing's prototype arm Phantom Works, said the technology marked "new era in modern warfare".
"In the near future, this technology may be used to render an enemy's electronic and data systems useless even before the first troops or aircraft arrive.
"We hit every target we wanted and made science fiction into science fact. When the computers went out, it actually took out the cameras as well. It was fantastic," Coleman said.