In the original album version, the song segues from "Have a Cigar" as if a radio had been tuned away from one station, through several others (including a radio play and one playing the opening of the finale movement of Tchaikovsky's Fourth Symphony), and finally to a new station where "Wish You Were Here" is beginning. The radio was recorded from Gilmour's car radio. He performed the intro on a twelve-string guitar, processed to sound like it was playing through an AM radio, and then overdubbed a fuller-sounding acoustic guitar solo.

Lyrically, the song is often considered to be a direct tribute to Syd Barrett. However, on the documentary The Story of Wish You Were Here, Gilmour and Waters separately describe the original concept that differs from this interpretation. Waters, who mainly wrote the lyrics complementing Gilmour's initial riff idea and subsequent joint composition, describes the lyrics as being directed at himself, as his lyrics often are.

Being present in one's own life and freeing one's self in order to truly experience life is a main topic in this song. Gilmour, on the other hand, recognizes that he does not ever perform the song without remembering Syd Barrett. Waters later adds that the song is nevertheless open to interpretation.

Lyrics

So, so you think you can tell

Heaven from Hell,

Blue skys from pain.

Can you tell a green field

From a cold steel rail?

A smile from a veil?

Do you think you can tell?

And did they get you to trade

Your heros for ghosts?

Hot ashes for trees?

Hot air for a cool breeze?

Cold comfort for change?

And did you exchange

A walk on part in the war

For a lead role in a cage?

How I wish, how I wish you were here.

We're just two lost souls

Swimming in a fish bowl,

Year after year,

Running over the same old ground.

What have we found?

The same old fears.

Wish you were here.