First, a run-down of the particulars:
- Due to potential metric conversion issues, a limit of 126 pounds was observed for this list.
- Inception of the championship occurred on 10/4/1996, the rematch between two top-ranked, undefeated fighters.
- Periodic inactivity was not an issue for Flyweights.
- Vacancies after permanent inactivity were filled by the next chronological winner in a Flyweight match. This was the perfect solution, as the permanent inactivity instances seen correlated with huge voids in known Flyweight history. I have a feeling that the other divisions won’t sort themselves out this easily.
Your current lineal Flyweight champion is Alexandre Pantoja
The full history is below. Note, the colored backgrounds indicate a title change.
| Date | Champion | Outcome | Challenger | Notes |
| 1996-10-04 | Mitsuhiro Sakamoto | WIN | Jin Akimoto | |
| 1997-04-06 | Mitsuhiro Sakamoto | WIN | Masaru Gokita | Sakamoto’s last qualifying fight. |
| 2001-09-27 | Homare Kuboyama | WIN | Toshiteru Ishii | |
| 2001-11-25 | Homare Kuboyama | WIN | Tomohiro Hashi | |
| 2002-03-13 | Homare Kuboyama | WIN | Takeyasu Hirono | |
| 2002-07-19 | Homare Kuboyama | WIN | Takeyasu Hirono | |
| 2003-03-18 | Mamoru Yamaguchi | WIN | Homare Kuboyama | |
| 2003-12-14 | Mamoru Yamaguchi | WIN | Yasuhiro Urushitani | 1st Shooto 56kg Championship bout |
| 2004-05-03 | Mamoru Yamaguchi | WIN | Hiroaki Yoshioka | |
| 2004-09-26 | Mamoru Yamaguchi | DRAW | Robson Moura | |
| 2005-01-29 | Mamoru Yamaguchi | WIN | Junji Ikoma | |
| 2005-09-23 | Mamoru Yamaguchi | WIN | Pat Seidel | |
| 2005-12-17 | Mamoru Yamaguchi | WIN | Daiji Takahashi | |
| 2006-03-24 | Mamoru Yamaguchi | DRAW | Shinichi Kojima | |
| 2006-05-12 | Mamoru Yamaguchi | WIN | Setsu Iguchi | |
| 2006-09-08 | Mamoru Yamaguchi | WIN | Erikas Suslovas | 9th Defense – Flyweight Record |
| 2006-10-14 | Shinichi Kojima | WIN | Mamoru Yamaguchi | |
| 2007-03-16 | Shinichi Kojima | DRAW | Yasuhiro Urushitani | |
| 2007-07-15 | Shinichi Kojima | WIN | Yasuhiro Akagi | |
| 2008-07-18 | Shinichi Kojima | WIN | Mamoru Yamaguchi | |
| 2009-01-18 | Shinichi Kojima | DRAW | Jesse Taitano | |
| 2009-03-20 | Shinichi Kojima | WIN | Yuki Shojo | |
| 2009-07-19 | Jussier da Silva | WIN | Shinichi Kojima | |
| 2010-06-12 | Jussier da Silva | WIN | Alexandre Pantoja | 1st Lineal bout outside of Japan |
| 2010-12-02 | Jussier da Silva | WIN | Danny Martinez | 1st Lineal bout in USA, not in Shooto |
| 2011-02-18 | Ian McCall | WIN | Jussier da Silva | |
| 2011-05-06 | Ian McCall | WIN | Dustin Ortiz | |
| 2011-08-05 | Ian McCall | WIN | Darrell Montague | |
| 2012-03-02 | Ian McCall | DRAW | Demetrious Johnson | |
| 2012-06-01 | Demetrious Johnson | WIN | Ian McCall | |
| 2012-09-22 | Demetrious Johnson | WIN | Joseph Benavidez | |
| 2013-01-26 | Demetrious Johnson | WIN | John Dodson | |
| 2013-07-27 | Demetrious Johnson | WIN | John Moraga | |
| 2013-12-14 | Demetrious Johnson | WIN | Joseph Benavidez | |
| 2014-06-14 | Demetrious Johnson | WIN | Ali Bagautinov | |
| 2014-09-28 | Demetrious Johnson | WIN | Chris Cariaso | |
| 2015-04-26 | Demetrious Johnson | WIN | Kyoji Horiguchi | |
| 2015-09-25 | Demetrious Johnson | WIN | John Dodson | |
| 2016-04-24 | Demetrious Johnson | WIN | Henry Cejudo | Ties Mamoru Yamaguchi with 9 title defenses |
| 2016-12-03 | Demetrious Johnson | WIN | Tim Elliott | |
| 2017-04-15 | Demetrious Johnson | WIN | Wilson Reis | |
| 2017-10-07 | Demetrious Johnson | WIN | Ray Borg | |
| 2018-08-05 | Henry Cejudo | WIN | Demetrious Johnson | |
| 2019-01-19 | Henry Cejudo | WIN | TJ Dillashaw | Henry Cejudo moves up in weight then retires |
| 2019-06-29 | Joseph Benavidez | WIN | Jussier Formiga | Vacant title, top contenders match |
| 2020-07-19 | Deiveson Figueiredo | WIN | Joseph Benavidez | |
| 2020-11-21 | Deiveson Figueiredo | WIN | Alex Perez | |
| 2020-12-12 | Deiveson Figueiredo | DRAW | Brandon Moreno | Figueiredo retains title in a draw |
| 2021-06-12 | Brandon Moreno | WIN | Deiveson Figueiredo | |
| 2022-01-22 | Deiveson Figueiredo | WIN | Brandon Moreno | |
| 2023-01-21 | Brandon Moreno | WIN | Deiveson Figueiredo | |
| 2023-07-08 | Alexandre Pantoja | WIN | Brandon Moreno | |
| 2023-12-16 | Alexandre Pantoja | WIN | Brandon Royval | |
| 2024-05-04 | Alexandre Pantoja | WIN | Steve Erceg | |
| 2024-12-07 | Alexandre Pantoja | WIN | Kai Asakura |