Scott Pruitt, a fierce critic of the agency, was approved by the Republican-controlled Senate despite Democratic attempts to delay the confirmation.
A judge in Oklahoma on Thursday ordered him to release, by Tuesday, emails he exchanged with oil and gas executives.
Democrats boycotted an earlier vote over his email refusal and claimed he was too close to energy companies.
They held the Senate floor through the night to put pressure on the chamber to delay the confirmation vote until the emails, which were exchanged while he was Oklahoma attorney general, were handed over.
But the Senate voted in favour of his confirmation by 52 to 46, and he was sworn in on Friday.
Mr Pruitt, 48, had refused to hand over the emails, at the request of a liberal watchdog, for more than two years.