Boogiepop Phantom is a dark mystery anime series which is often compared to Serial Experiments Lain. The series is 12 episodes long, but the story is not told in a linear fashion. The episodes centre around different characters who sometimes have just a short involvement in the major events of the series. For this reason, many scenes are seen twice, from different perspectives, and some episodes are out of sequence, although there is a slow general time progression.

The story centres around several important characters, most of whom are students from one of two high schools in the city in which the series takes place. The city (which is never named) was held in fear by a serial killer five years ago, who was never caught. When the series begins, high school students have just started to disappear again, and the blame is placed by many on Boogiepop, a mysterious entity who is said to be Death.

Boogiepop Phantom is based on the series of books Boogiepop by Kouhei Kadono. The original character designs are also done by the books' illustrator, Kouji Ogata.