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Kooks vocalist Luke Pritchard found himself writing lyrics containing a lot of emotional drama for their third album and the phrase "junk of the heart" kept coming back to him. He told Spin magazine: "Even before we went to record, I wanted to name the album that. It made sense. The songs lyrically are about baggage, my 'Junk of the Heart.' I got very obsessed with the relationship between pain and love, and how you can't have one without the other. 'Junk of the Heart' represents that for me in one phrase."
This song is the album's title track and second single. During the writing of Junk of the Heart (Happy) Pritchard became "obsessed" with the French electronic duo Air and they were a significant influence on this song's sound. He told Spin: "The synthesizers on 'Junk of the Heart' all came from that desire for the eerie and nostalgic feel you get on Air's record. When I was writing the last two Kooks records I was inspired by music from the '60s and '70s. But for this album, the whole idea was to rethink it and make it really modern."