Egyptian Foreign Minister Sameh Shoukry announced the recovery of the artifact, known as the "Green Sarcophagus", during a televised press conference Monday.
He said it had been surreptitiously removed from the country and its recovery is part of efforts to "protect Egypt's heritage".
The lid, measuring nearly three metres (3.3 yards) in length and 90 centimeters in width, was among 17 artifacts recently recovered from the United States, Tourism and Antiquities Minister Ahmed Issa said at the news conference.
The sarcophagus lid was looted from the Abusir necropolis south of Cairo then transported to the US in 2008, eventually making its way to the Houston Museum of Natural Science in 2013, according to state media.
Only the lid had been stolen, he added, as the whole coffin weighs about half a ton, making it one of the largest wooden sarcophagi from Ancient Egypt.
Mostafa Waziri, the secretary-general of Egypt's Supreme Council of Antiquities, said the sarcophagus likely belonged to a nobleman.
He said it dates back to the Late Period of Ancient Egypt, and it was named the Green Sarcophagus because of the color of the face etched on it.
In addition to the latest recovered artefacts, Egypt has unveiled more than 300 sarcophagi and 150 bronze statuettes over the past two years, some of them dating back more than 3,000 years.
Over the past decade, Egypt has recovered about 29,000 antiquities found to have been taken abroad through illegitimate means.
They were among major discoveries made that the authorities hope will help revive the country's vital tourism sector, hit hard after the Covid pandemic and previous unrest.