The Arisaka was based around the basic German Mauser design, albeit with some local alterations. It utilized a cock-on-closing action, which improved the rate of fire from the standard Mauser cock-on-open design. It featured a quick-release bolt and antiaircraft sights, as well as a rotating bolt cover and monopod. The bolt cover, in particular, was highly problematic. Many soldiers simply discarded them. The original versions are generally considered to be very strong rifles, having one of the strongest receiver assemblies of any military rifle of its time. As a bolt action rifle, the Type 99 was a very solid weapon, but was completely outclassed by the semi-automatic rifles deployed by the Allies in that theatre of war.

The Type 99's bayonet was in the form of a very long, slender blade, grooved to provide rigidness. The early models featured a hooked quillion. These bayonets attached to a lug under the barrel and were further stabilized by a loop that fit around the muzzle. Unmounted, it handled similar to a machete.