The music video opens with a group of schoolchildren on board a coach. The camera focuses on a young girl who opens a medical book of pictures of the human skeleton. A blond boy spits on the page, then smiles at her as he walks away. The children go to the Natural History Museum, where the same boy tries to scare the girl with a skull in his hood. She chases the boy in the museum, but falls near the bottom of a flight of stairs and sprains her wrist. At the hospital, she gets an X-ray of her hand. It then shows her brushing her teeth whilst picturing herself as only bones. The background behind her morphs into a toilet area at the Ministry of Sound nightclub, South London. When she reverts into a person, she is older. She passes a couple having sexual intercourse in a stall, but she only sees them as skeletons (this shot is omitted from some pre-watershed television edits of the video). She exits the bathroom and heads to the nightclub's bar, where a man (uncredited appearance of Rick Warden) flirts with her. You can barely hear his lines under the music. She then pictures him as a skeleton and feels his jawbone before leaving. She then goes to the dance floor, and sees more people as skeletons, almost as if she has X-ray vision. She exits the nightclub, and the Chemical Brothers themselves make a brief cameo appearance, stepping out of a taxi with DJ equipment. She then steps into that same taxi, where she sees the driver as a skeleton. He then asks her 'Where you going, baby?' in a camp, droll voice.
In October 2011, NME placed it at number 50 on its list "150 Best Tracks of the Past 15 Years", writing that the song "[starts] with a menacing, trance laden groove" and "[builds] to an absolute dance stomper".
In an interview with BELPOP, Lords of Acid founder Praga Khan confronted The Chemical Brothers backstage over the techno beat used in "Hey Boy Hey Girl" that is identical to "I Sit On Acid 2000" released by Lords of Acid. Their response to the allegations was "Everyone steals from everyone."