An F-35 Lightning II, also known as the Joint Strike Fighter, flies over California in May 2010
The in-development F-35 Joint Strike Fighter programme is believed to have cost $400bn
A grand jury in the US state of Connecticut charged Mozaffar Khazaee, 59, with two counts of transporting stolen goods.
He was arrested on 9 January for trying to smuggle thousands of pages of F-35 Joint Strike Fighter documents.
If convicted, he faces up to 20 years in prison.
Mr Khazaee is accused of transporting, transmitting and transferring in interstate commerce goods obtained by theft, conversion or fraud, according to court documents.
He is said to have stolen the sensitive materials from defence contracting companies where he was employed, Connecticut US Attorney Deirdre Daly told US media on Tuesday.
The engineer is an ex-employee of military contractor Pratt & Whitney and in that capacity was responsible for carrying out strength tests on engine parts, US media have reported.
He was made redundant from a defence contractor in August, prosecutors said.
The investigation began in November, when customs officials and homeland security agents intercepted a shipment Mr Khazaee sent from Connecticut to a freighter in Long Beach, California, bound for Hamadan, Iran, according to court records.
The shipment was marked as containing household goods, but officials instead found boxes of documents containing technical manuals and proprietary material related to the F-35 programme.
Mr Khazaee was arrested on 9 January at the airport in Newark, New Jersey, on his way to Iran.
The former Connecticut resident is reportedly being detained in New Jersey pending his arraignment.
The F-35 Joint Strike Fighter – the most expensive defence programme in history – is estimated to have cost approximately $400bn (£242bn)