"[6] Featured in the opening credits of the 2004 film Napoleon Dynamite, writer/director Jared Hess commented that, originally, they could not find the song they were looking for, but wanted to use "We're Going to Be Friends", so a copy of Napoleon Dynamite was sent to The White Stripes, who promptly approved the song's use in the film.

[9] Singer-songwriter Jack Johnson recorded a cover of the song on his album Sing-A-Longs and Lullabies for the Film Curious George.

[citation needed] Bright Eyes covered the song with guest First Aid Kit for the charity album Cool for School: For the Benefit of the Lunchbox Fund.

The song is also featured in the Life in Pieces episode "Sexting Mall Lemonade Heartbreak".

CBS included a song in commercials for its 2006 program The Class that resembled the tune of "We're Going to Be Friends.

[12] A portion of the song is also the opening theme to his podcast, Conan O'Brien Needs a Friend.