- Andrea Migno (Sky Racing Team VR46) starts from pole for the first time in his grand prix career in his 42nd GP start. He is the sixth different Italian rider this year to line up on pole in the Moto3™ class.
- Newly crowned World Champion Brad Binder (Red Bull KTM Ajo) starts from second place on the grid – his seventh front row start of the year.
- Enea Bastianini (Gresini Racing Moto3) is on the front row for the eighth successive race. Bastianini has been on the podium five times already in 2016, but has not stood on the top step since the San Marino GP last year.
- Hiroki Ono (Honda Team Asia) heads the second row of the grid after being the fastest rider in qualifying and then being penalized three grid positions. This is the best grid position in the lightweight-class for a Japanese rider at Motegi since Tomoyoshi Koyama was second fastest qualifier for the 125cc race in 2007. Ono will be aiming to be the first Japanese rider in the lightweight-class to finish on the podium at his home GP since Youichi Ui won the 125cc race at Motegi in 2001.
- Nicolo Bulega (Sky Racing Team VR46) will start from fifth place on the grid on the day that he celebrates his 17th birthday.
- Starting from sixth place on the grid is Lorenzo Dalla Porta (Sky Racing Team VR46) – his best qualifying result so far in his grand prix career.