Round 3 was held as a replacement for the Autopolis round in Kyushu, which had been scheduled for 26 April but was cancelled due to rain. The starting grid was based on the official qualifying results from 25 April, with the race run as a sprint over 25 laps or a maximum of 50 minutes, with no mandatory tyre change.

Ayumu Iwasa (TEAM MUGEN AUTOBACS) started from pole position, followed by Kakunoshin Ohta (DOCOMO TEAM DANDELION RACING) and Tomoki Nojiri (TEAM MUGEN AUTOBACS), giving Honda/M-TEC-powered drivers the top three places on the grid. Ren Sato (PONOS NAKAJIMA RACING) lined up in seventh, Tadasuke Makino (DOCOMO TEAM DANDELION RACING) eighth and Igor Omura Fraga (PONOS NAKAJIMA RACING) ninth.

Round 3 Race

At 10:00am, when the race began at Fuji Speedway, the air temperature was 29°C and the track temperature was 34°C. Although the rain that had continued since the previous day had stopped, wet patches remained in places around the circuit.

Iwasa made a slow start from pole position, allowing Ohta to lead into Turn 1. Behind them, Sena Sakaguchi (Toyota) made a strong getaway and moved into second around the outside, followed by Nojiri and Makino. Fraga also started well from ninth and moved up behind Makino before overtaking him under braking for Dunlop Corner to take fourth.

Several cars, including the slow-starting Iwasa, made contact immediately after the start, leaving Iwasa stopped beyond Turn 2. The Safety Car (SC) was deployed and remained on track until the end of Lap 9.

The race resumed on Lap 10. Nojiri, running in third, drew alongside Sakaguchi before Turn 1, while Fraga accelerated rapidly in the slipstream of the two cars to make it three-wide. Meanwhile, race leader Ohta and second-placed Sakaguchi ran onto a wet patch around the outside of Turn 1 and overshot the corner. Fraga took advantage, passing Nojiri on the inside to take the lead. Nojiri moved into second, followed by Sakaguchi in third, Ohta in fourth and Makino in fifth.

On the following lap, Juju (HAZAMA ANDO Triple Tree Racing) went off after contact and stopped on the circuit, prompting a second SC period.

The race resumed on Lap 15, with Fraga making a strong restart and immediately opening a substantial gap over second-placed Nojiri to retain the lead. Ohta passed Sakaguchi to move into third, but was then handed a 10-second time penalty for a breach involving alteration of the track surface on the grid, effectively dropping him well down the order.

Fraga continued to extend his advantage over Nojiri and controlled the remainder of the race, taking the chequered flag after 25 laps. Nojiri finished second, Makino fourth, Ohta eighth and Sato ninth, with each scoring championship points under the revised points system awarding points from P1 to P9 in Round 3.