The was the eleventh season having a fourth-tier status in Japanese football and the 26th season since the establishment of the Japan Football League.
No team was promoted from the JFL to the J3, since none of the top four clubs last season met the needed requirements for promotion, which includes (but not limited to) having a J3 license.
Tochigi City, 2023 Kanto Soccer League runner-up, was the sole promoted team to the JFL as they won the 2023 Regional Champions League.
Vonds Ichihara could join Briobecca Urayasu as Chiba's representatives in the JFL, had they won the 2023 JFL play-off against Okinawa SV.
This season is the second to feature promotion/relegation between the J3 League and the Japan Football League, enabling the possibility for teams to be relegated from the J3. The system of promotion/relegation between the leagues can be determined by the eligibility (Promotion to J3 requires a J.League license) of the JFL's champions and runners-up for the season.
No changes were made from the previous season:
The dates and the host teams of the promotion/relegation play-off were pre-determined by the J.League. In case it happens: It will be played in two legs on 1 and 7 December, with the J3 team hosting the second leg; away-goals rule will not be applied; should the match be tied, it will require extra-time, and if the draw persists, penalty shoot-outs.
Tokyo Musashino United FC returned to its former name Yokogawa Musashino FC, and Suzuka Point Getters became Atletico Suzuka Club.
The teams which possess (or are applicants of) promotion-enabler licenses are highlighted in green in the following table.
The play-offs, officially called the 2024 J3/JFL Play-offs (), took place on 1 and 7 December 2024. If the two teams were equal on the scoreboard, the match would go to extra time and penalties. Away goals rule would not be applied.
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Kochi United SC won the J3/JFL play-offs on aggregate 3-1 and got promoted to J3, while YSCC Yokohama lost the play-offs and got relegated to JFL.
The play-off (') took place on 1 December 2024.
Minebea Mitsumi stayed in the JFL; Vonds Ichihara stayed in the Kantà  Soccer League Division 1.