A machine in a specially-equipped van took the images while parked near his underground tomb in the Valley of the Kings.
Around 1,700 images were taken during the 15-minute scan, and researchers hope they will provide the key to questions surrounding his life and death, including his royal lineage, his exact age – now estimated at 17 – and the cause of his death.
King Tutankhamun’s toes and fingers and an eerie outline of his face could be seen as the scans were taken.
A simpler x-ray taken 36 years ago showed bone fragments inside his skull, but was not sophisticated enough to determine whether they signified a blow to the head.
King Tut was buried in a “hurried” fashion in a glitter of gold treasures, according to Egypt’s chief archaeologist Zahi Hawass.
“There are so many stories about his death and his age,” Mr Hawass said.
“Today we will determine what really happened.”
The CT scan will provide a far more detailed, three-dimensional view of the scattered bones and coverings that make up Tut’s mummy.
This form of imaging has been used for a number of Egyptian mummies in the past, including one of famed pharaoh Ramses I.
It also was used on the 5,200-year-old remains of a Copper Age man found frozen in 1991 in a glacier in the northern Italian Alps, where it identified an arrowhead in the iceman’s body that possibly killed him.
The results of the Tut scan will be announced later this month in Cairo.
Mr Hawass said it is the first time the mummy has been removed from its tomb in 82 years and is in bad condition.
He said Egyptian officials will begin a “process of restoration to protect and preserve it”, which will be done inside the tomb itself.
Tutankhamun’s short life has fascinated people since his tomb was discovered in 1922 by British archaeologist, Howard Carter, revealing a trove of fabulous treasures in gold and precious stones that showed the wealth and craftsmanship of the Pharaonic court.
Mr Hawass said Carter’s team damaged the mummy as they used sharp tools to prize off the famous gold and blue mask.
Tutankhamun ruled about 3,300 years ago and is believed to have been the 12th ruler of ancient Egypt’s 18th dynasty.
He ascended to the throne at about the age of eight and died around 1323 BC at approximately age 17.