U.N. Squadron was ported to the Super Nintendo Entertainment System and Super Famicom in 1991 by Capcom. While it follows the same layout as the Arcade game, it includes many changes exclusive to this version.
The first major change is on the mission structure. Instead of following missions linearly, the player can now choose from available missions on a map, being able to tackle them on any order. Once a set of missions is completed, an area of the map is conquered thus unlocking another set of missions, which are represented by points on the map. Some of the missions are represented by airplane icons, corresponding to enemy aerial attacks; these will actually move on the map towards the Area 88 icon whenever the player complete or fails a mission. This version also adds exclusive missions, as well as special missions where you destroy enemy convoys for extra money. When you lose a life, you are taken back to the map screen and must try the mission again.
The game's shop has also been overhauled in this port. Ships aren't tied to the characters anymore, as you now start with the F-8E Crusader and must buy new ships on the shop. You now also have all secondary weapons available from the start instead of them being tied to the current mission. You can buy any weapon as long as your current ship can handle it, and you're also able to carry more than one weapon, being able to switch them in the mission by pressing the X button.