Halee started working as a cameraman for CBS Television in the 1950s. He was also studying to be a classical trumpet player.
He became an audio engineer for CBS Television, working on many shows and the top rated The $64,000 Question TV quiz show.
As television shows moved to the West Coast, he lost his job in a union dispute and layoff at CBS Television. He went to work for Columbia Records in New York as an editor and later as a studio engineer, working with Bob Dylan, including the first long-format radio single, "Like a Rolling Stone".
Halee discovered that the uniqueness of Simon & Garfunkel harmonies could only be achieved by recording both voices on the same microphone at the same time. That technique did well, as the song "Mrs. Robinson", from the 1968 album The Graduate, won him a Grammy Award.
He was best known for producing several albums with Simon & Garfunkel. He is mentioned in their 1965 song "A Simple Desultory Philippic (or How I Was Robert McNamara'd into Submission)", written by Paul Simon. He also co-produced Simon's first solo album after the Simon & Garfunkel years and went together with Simon to South Africa in 1985 to record something new that "wasn't written yet, we were going with nothing, so it was a gamble. A lot of people thought we were nuts", Halee says. It led to the Grammy Award-winning album Graceland. "I was having a ball recording these guys. For a guy from my background, everything was so organised generally. Here in the rawness of this, the earthiness, I was in seventh heaven." After Graceland, Roy Halee continued travelling with Simon as an engineer, this time to Brazil and West Africa, which resulted in the album The Rhythm of the Saints, with "all congas, bass drums, bata...everything imaginable."