The 21-year-old, a member of Japan's silver medal-winning men's 4x100 relay team at the Rio Olympics, shattered the previous record by 0.02 secs at an intercollegiate meet in Fukui, central Japan.
The Toyo University student started moderately in the final but raced past his rivals in top gear and finished first with a 1.8-metre tailwind.
Kiryu screamed with joy after crossing the line and pointed to a display clock showing his time.
"I'm thrilled to have done it in my last 100 race of the season," said Kiryu, according to Kyodo News.
More From This Section
"I'm on the starting block of the world now that I've run a nine," he added.
Kiryu, who ran a wind-assisted 9.87 in the 100m in 2015, had long competed with his domestic rivals, including Japan teen sensation Abdul Hakim Sani Brown, to achieve the national feat.
Japan's previous national record of 10.00 was set by Koji Ito in 1998. Ito's time was the Asian record until 2007 when Nigerian-born Qatari Samuel Francis streaked over the line in 9.99.