| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts | Promotion, qualification or relegation |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Kochi United | 13 | 11 | 0 | 2 | 25 | 8 | +17 | 33 | |
| 2 | Tiamo Hirakata | 13 | 8 | 1 | 4 | 23 | 19 | +4 | 25 | |
| 3 | Tochigi City | 13 | 7 | 2 | 4 | 25 | 19 | +6 | 23 | |
| 4 | Honda FC | 13 | 6 | 4 | 3 | 15 | 8 | +7 | 22 | |
| 5 | Veertien Mie | 13 | 5 | 6 | 2 | 18 | 14 | +4 | 21 | |
| 6 | ReinMeer Aomori | 13 | 4 | 7 | 2 | 16 | 10 | +6 | 19 | |
| 7 | Okinawa SV | 13 | 5 | 4 | 4 | 23 | 21 | +2 | 19 | |
| 8 | Reilac Shiga | 13 | 5 | 3 | 5 | 17 | 12 | +5 | 18 | |
| 9 | Verspah Oita | 13 | 4 | 5 | 4 | 16 | 18 | −2 | 17 | |
| 10 | Atletico Suzuka | 13 | 5 | 1 | 7 | 19 | 18 | +1 | 16 | |
| 11 | Maruyasu Okazaki | 13 | 4 | 4 | 5 | 17 | 19 | −2 | 16 | |
| 12 | Sony Sendai | 13 | 4 | 3 | 6 | 15 | 18 | −3 | 15 | |
| 13 | Briobecca Urayasu | 12 | 3 | 2 | 7 | 13 | 16 | −3 | 11 | |
| 14 | Yokogawa Musashino | 13 | 3 | 3 | 7 | 10 | 21 | −11 | 12 | |
| 15 | Criacao Shinjuku | 13 | 2 | 4 | 7 | 8 | 23 | −15 | 10 | Qualification for relegation playoffs |
| 16 | Minebea Mitsumi | 12 | 1 | 3 | 8 | 8 | 24 | −16 | 6 | Relegation to the Regional Leagues |
Updated to match(es) played on 16 June 2024. Source: Japan Football League
Rules for classification: 1) Points; 2) Goal difference; 3) Goals scored; 4) Head-to-head points; 5) Head-to-head goal difference; 6) Head-to-head goal scored; 7) Fair-play points.
Rules for classification: 1) Points; 2) Goal difference; 3) Goals scored; 4) Head-to-head points; 5) Head-to-head goal difference; 6) Head-to-head goal scored; 7) Fair-play points.
Promotion is conditional on holding a valid J3 license (marked in bold in the table). If two clubs with J3 license finish in the top two of the JFL, the 1st-placed JFL club is automatically promoted to the J3 League and the 20th-placed J3 club is relegated to the JFL. The 2nd-placed JFL club will play the 19th-placed J3 club in the J3 and JFL promotion/relegation playoffs, and the winner will be in the J3 League.
If there is only one club with a J3 license in the top two places in the JFL, the licensed club will be automatically promoted to J3 if the licensed club is ranked 1st in the JFL, and the club ranked 20th in J3 will be automatically relegated; if the licensed club is ranked 2nd in the JFL, it will play off with the club ranked 20th in J3. In this case, the club ranked 19th in J3 will remain in the J3 League. If the 1st- and 2nd-placed clubs in the JFL do not both have J3 license, there will be no swap between J3 and JFL.