The track comes off Apple's first album in seven years The Idler Wheel..., co-produced with musician Charley Drayton.
Directed by Joseph Cahill, the video features several surreal vignettes of Apple amongst creatures including squid, alligators and snails.
Apple told Pitchfork that she and Cahill's concept behind the video was "just to come up with a bunch of things and do things to me and put me in situations and surprise me".
She added: "One thing I wanted to have happen was to be covered in snails. I laid in a bed of soil and they put snails all over me. And then they brought in [stuff] that I would not have asked for. He put a dead squid on my head."
The Idler Wheel... is set for a June 19 release.
Watch the video for Fiona Apple's 'Every Single Night' below: