All regional champions qualified for the Japanese Regional Football Champions League. Like the J.League, there was no relegation in this season to Prefectural Leagues (promotion and relegation between divisions were still available for some regions).
Updated to match(es) played on 27 September 2020. Source: Soccerway, Hokushinetsu Football League Rules for classification: 1) Points; 2) Goal difference; 3) Goals scored
Division 2
Tōkai
Owing to the coronavirus pandemic, the Tōkai region played a knockout tournament to decide the team qualifying for the 2020 Regional Promotion Series (for Division 1 only).
In Division 1, Yazaki Valente did not participate, so Kariya received a bye to the semi-finals.
In Division 2, Bombonera Gifu did not participate, so Toyota received a bye to the semi-finals.
Updated to match(es) played on unknown. Source: Soccerway Rules for classification: 1) Points; 2) Goal difference; 3) Goals scored
Division 2
Chūgoku
Due to the coronavirus pandemic, the Chūgoku region played in a tournament known as the CSL Championship 2020, or C-1 Cup, with 8 teams competing for a spot in the 2020 Regional Promotion Series.
NTN Okayama and Dezzolla Shimane did not participate in this season.
On August 11, the Kyushu League was abandoned, due to Kaiho Bank's withdrawal and the spread of coronavirus in Okinawa and Kumamoto. Okinawa SV, as the 2019 Kyushu League champions, are elected to play in the Regional Promotion Series.