Writer Bill Tobelman argues that the inspiration for "You're Welcome" may have derived from Brian Wilson's attempt to turn his band mate Al Jardine onto LSD while giving him a car ride, which was followed by Wilson circling the car around multiple times until he finally let Jardine go.
The song is a mostly-a cappella chant, with the repeating phrase of "Well / you're well / you're welcome to come". In mid 1967, Mike Love said of the piece "[It's] incredible. The title is 'You’re Welcome'. No other lyrics. I don’t know how Brian did it, but there’s no accompaniment. [sic] 'Heroes and Villains' is going to be released as the first single on our new label, Brother Records…We are finishing it [the album] now." Its "extraordinary long fade-in" gives the impression of development which is absent from the similar "Whistle In", writes Daniel Harrison.