The E train is one of only three lines of the New York City subway to be underground along its entire route (a feat it shares with the C and R Trains), and one of only three lines that is entirely on trackage built by the city operated Independent Subway System (a feat matched by only the C and G Trains).

Most of the route of the E was part of the original Independent Subway System construction in the early 30s, including the Eighth Avenue line (home also to parts of today's A and C Trains), the portion under 53rd street and under the 53rd street East River tunnel (which the E shares with today's F Train), and the Queens Boulevard line (which is home to portions of today's F, R, and G Trains). Only the short distance from where the E leaves the old Queens boulevard line at Briarwood to the terminal at Jamaica center was built later.

After several incarnations, a route on this trackage running from the Hudson Manhattan Terminal in lower Manhattan, local up the Eighth Avenue, across 53rd street and through the tunnel to Queens, and express on the Queens Boulevard line received the letter designation E. I believe this is a rather recent route letter designation, perhaps dating to the 70s. After the completion of the World Trade Center that station was renamed accordingly, and still serves as the Manhattan terminal of the E.

The farthest outlying portion of the E line in Queens, from where the E leaves the Queens Boulevard line at Briarwood three stops to the terminal at Jamaica Center is some of the newest and most unique construction on the New York City subway. Completed in the 80s, the tunnels are alabaster concrete and the stations are extremely bright, cavernous, modern edifices that resemble certain stations on the BART more than most stations of the New York City subway.

The E train runs a mix of R32 and R44-46 rolling stock. The R32s are 65' cars from the early 60s and really show their age, updated with a comical blue bulb route letter display that looks like a sorry attempt to replicate LED. They will soon be retired. The R44s are nicely appointed 75' cars from the early 70s.