After becoming a freelancer for a short time, he joined Logistics where he worked in the software development section and was responsible for animation work and later developing tools for animation work in games. While working in Logistics' animation department he started Team Till Dawn in 2002, which was also the beginning of his career as anime director.
Kishi is known for directing anime series, such as Yugo the Negotiator, Ragnarok: The Animation, Angel Beats!, Magikano, My Bride is a Mermaid, Persona 4: The Animation and Aura. Also, he worked as anime director alongside his partner and anime screenwriter Makoto Uezu as story composer in animes such as Fate/Prototype, Danganronpa: The Animation, Devil Survivor 2: The Animation, Arpeggio of Blue Steel: Ars Nova, Kamisama Dolls, Tentai Senshi Sunred and Carnival Phantasm.
For the Harmony Unleashed: Extreme Ignition film series produced by Ivanna The Movie, OLM Digital and Bandai Visual, Kishi will direct the film series and coming back with Makoto Uezu as screenplay writer. Also, Seiji will be directing the animated cutscenes for Rainbow Dawn Dissidia as well as the OVA (with screenplay by Akatsuki Yamatoya)