The object of Bosconian is to score as many points as possible by destroying enemy bases and ships. The player controls a small fighter ship that can move in eight directions and can fire both forward and backward. Each level consists of a number of green space stations that must all be destroyed to advance to the next level (a semi-transparent mini-map helps identify their location). Each station consists of six cannons arranged in a hexagon, surrounding a central core. The player must either destroy all six cannons or shoot the core to destroy a station, and in later levels the core is capable of defending itself.

Additionally, the player must avoid or destroy asteroids, mines, and a variety of enemy missiles and ships that attempt to collide with the player's ship. Enemies occasionally launch formation attacks — destroying the leader causes all remaining enemies to disperse, but destroying all enemies in a formation scores extra bonus points. A spy ship (worth a random bonus value) also appears occasionally, which must be destroyed or the enemies will go berserk.