The HondaJet is unique among the (small) bizjets as the HondaJet has jet engines mounted on top of the wings, like the VFW614! For the rest, the basic features are like many other bizjets, with low mounted (slightly) swept wings and a T-tail. Rather typical is the nose, with a slight pelican beak shape, and the cockpit window configuration. The gears are all single wheel, and the airplane has tall winglets. Finally, the HondaJet has a tail cone that can be opened to act as a speed brake, compensating for the lack of thrust reversers.

This is the basic, original version of the HondaJet. It can be recognised by the small wing fences in the wing leading edge, at roughly one metre from the wing tips.

On the first improved version, dubbed the HondaJet Elite, the small wing fences in the wing leading edge, are gone. Also the span of the horizontal stabiliser is slightly larger, but probably not clearly visible. An upgrade package for pre Elite aircraft is also known as APMG, Advanced Performance Modification Group.

The HondaJet Elite S is a further improved version with a higher maximum take-off weight, updated avionics and a new paint scheme.

The 2022 upgrade is called Elite II. This version has spoilers on top of the wings that are deployed after landing to reduce the landing run. Other new features appear to be only inside, but time will learn.