Sanxion is a side-scrolling shoot ’em up, the goal to traverse each level from left to right avoiding or destroying any enemies and obstacles. The side-scroller speed is controllable, increasing the closer the player is to the center of the screen. The screen is divided in two sections, the upper one with an overhead view, and the lower one, taking up two-thirds of the screen, shows a typical side view. Enemies can come from both sides of the screen in close formations that the player must avoid colliding with.
One notable aspect of this game is that while it is automatic scrolling, for the most part, the player can control the speed of the engines (there is even a bonus timer that counts down, as an incentive for those who want to “blast through”), and the pitch of the noise alters accordingly, while sounding vaguely like a didgeridoo. This “adjustable rate autoscroll” is uncommon in the genre. Several levels end with sections where the ship is forced to fly at maximum speed (a two-note siren will sound at the beginning of such sections), where the player must be quick to avoid oncoming barriers.
There are two main types of levels in Sanxion, based on the enemies. In some, such as the first, the enemies are constant throughout the level. In some others, such as the second, reaching a certain point (usually change of terrain) will cause all enemies on screen to self-destruct, and a different type of enemy will appear. There are exceptions to these patterns.
At the end of each level, there are non-lethal bonus stages which award points to the player for shooting, crashing or avoiding floating letters (the action required depends on the actual letter) at great speed. The background in these stages is rainbow, and the “radar” does not show your ship.