On Sunday, 24 May, sunlight broke through thin cloud cover at Suzuka Circuit, with the air temperature rising to 24°C and track temperature to 33°C by the start of qualifying.

In the regular two-stage knockout qualifying format, the drivers who advanced from Q1 to Q2 were Ren Sato (PONOS NAKAJIMA RACING), Tadasuke Makino (DOCOMO TEAM DANDELION RACING), and Tomoki Nojiri (TEAM MUGEN AUTOBACS) from Group A, and Ayumu Iwasa, Kakunoshin Ohta, Igor Omura Fraga (PONOS NAKAJIMA RACING), and Yuto Nomura (San-Ei Gen with B-Max) from Group B. In Q2, where 12 cars battled for pole position, Iwasa secured P2 while aiming for consecutive pole positions. Makino, making his first Q2 appearance in some time, took P3, with SUPER FORMULA rookie Nomura qualifying P4. However, a series of track limits penalties changed the final order. Omura Fraga lost his third-fastest time and dropped to P10, while Ohta, Sato, and Nojiri were demoted to P9, P11, and P12 respectively.