The iconic red brick station building appears in the opening sequence and several transition scenes. Its historic Marunouchi side facade is particularly prominent when showing the characters' daily work routine in central Tokyo.

The bustling Shinjuku district serves as a key location where several important scenes take place. The neon-lit streets and crowded atmosphere reflect the anime's urban setting and the hidden supernatural world within modern Tokyo.

This major JR station in western Tokyo serves as a model for several urban scenes in the series. The station's modern architecture and busy atmosphere perfectly capture the metropolitan setting where Academy City's events unfold.