- Goemon - the main protagonist and titular character of the series.
- Ebisu - She's the best friend to the Goemon in the future. She wields the same weapons as Ebisumaru and possibly is his daughter.
- Yui - A equivalent of Yae. She wields the same weapons as Yae.
- Sasuke - A clockwork robot ninja. She wields the same weapons as Sasuke.
- Hanzo - the first boss of the first stage: Haikyo.
- Kojirou - the second boss of the second stage Yami.
- Benkei - the third boss of the third stage Chugi.
- Musashi - the fifth boss of the fifth stage: Oni, before the main boss: Yoshitsune's Black Impact.
- Yoshitsune - one of the main antagonists, he was a first encountered as fourth boss of the fourth stage: Mato, and the second encountered as the giant impact called Black Impact, the sixth boss of the fifth stage: Oni.
- Kiyohime - one of the main antagonists and final boss of the game.
- Area 1 / Haikyo - Boss: Hanzo - Hanzo's Hide Impact
- Area 2 / Yami - Boss: Kojirou
- 'Area 3 / Chugi - Boss: Benkei - Benkei's Heavy Impact
- Area 4 / Mato - Boss: Yoshitsune
- 'Area 5 / Oni - Boss: Musashi - Yoshitsune's Black Impact
- Area 6 / Naraku - Final Boss: Kiyohime