The front cover features a photo of Donald Fagen as a disc jockey, speaking into a RCA 77DX microphone. In front of him is a turntable, an ashtray, a matchbook, and a pack of Chesterfield King cigarettes. Visible on the table with the record player is the cover of the 1958 jazz album Sonny Rollins and the Contemporary Leaders (one of Fagen's favourite albums).

The cover was shot in Fagen's apartment in the Upper East Side of Manhattan by photographer James Hamilton. Two shoots were arranged because in the first, the RCA microphone was facing the wrong direction. Gale Sasson and Vern Yenor are credited with the cover's set design.

On the wall behind is a large clock, indicating that the time is 4:09.

An advertisement in Billboard shortly before the album's release described the album cover: "At 4:09 A.M., silence and darkness have taken hold of the city. The only sound is the voice of The Nightfly".

Fagen appeared on the album cover despite his reclusive nature. "It was an autobiographical album so it seemed like I might as well go public with it," he said.

The back cover of the album depicts a house with a solitary window lit. Maybe one of the listeners to the radiostation. The Nightfly at 4:09 A.M.

Commentators took this also as a memory of Fagen's youth as a teenager?

Robert Palmer, of The New York Times, continued in this line of thinking: "Inside, there's a teenager with his ear next to a portable radio. He's playing it softly, so his parents won't wake up, and he can barely make out the sounds through the static."

Donald Jay Fagen (born January 10, 1948) is an American musician who was the co-founder, lead singer, co-songwriter, and keyboardist of the band Steely Dan, formed in the early 1970s with musical partner Walter Becker. In addition to his work with Steely Dan, Fagen has released four solo albums, beginning with The Nightfly in 1982, which was nominated for seven Grammys.

In 2001, Fagen was inducted into the Rock and Roll Hall of Fame as a member of Steely Dan. Following Becker's death in 2017, Fagen continued to tour alone under the Steely Dan name.

Steely Dan