Chopper pilot David Keith Martz, 49, was charged with reckless operation of an aircraft, landing an aircraft on a public road and landing an aircraft without a permit for the July 7 incident, TMZ.com reported.
Lee had hired the chopper to take him to and from the Nine Inch Nails concert at the Verizon Wireless Amphitheatre in Irvine.
The Los Angeles Police Department received complaints about a helicopter hovering over Lee's Hollywood Hills home, but when Air Support Division officers tried to contact Martz, he had by then landed on the public street out front and already entered Lee's house, TMZ.com said.
He later came out with Lee and two companions, and flew them to the rock show, the report said.
Martz faces a maximum six months in jail and a $1,000 fine on each count, if he's convicted.
Selena Gomez drops F-bomb, walks off stage during Jingle Ball performance
Wisconsin business offering 'therapeutic cuddling' forced to close