An upgraded version of Metal Slug 2, titled Metal Slug X, was released in March 1999 for the Neo Geo MVS. It fixed slowdown problems from the original game, and increased the difficulty. Metal Slug X also introduced some new elements to the game system;

• Much of the music has been remixed or altered.
• A new announcer
• Many stages have the time of day changed. Instead of individual levels being set at either day or night, the stages can take place at dusk, twilight, or sunset.
• It is now possible for the player character to become fat by collecting food items in every stage after Mission 2; in the original game, the obese transformation was only possible in Mission 4.
• All levels contain an increased enemy count and new enemy placements, as well as different enemy characters, and new boss placements.
• Vehicle types and locations are different.
• There are more power-ups, POWs, and items (particularly food) in each mission. These items are often hidden.
• Many environmental elements have different reactions when shot, such as exploding with unexpected results or randomly spewing out items or enemies.
• Stronger versions like the heavy machine gun, flameshot, shotgun, laser rifle, and rocket launcher are available. Each deals more damage than their normal counterpart, has a different appearance and a wider (or longer) area of impact. If the player happens to be fat while using these heavier weapons, they appear differently and can cause even more damage.
• Several new weapons are included: Stones, Iron Lizard, Enemy Chaser, Super Grenade, Drop Shot, and a new Golden Metal Slug, which is available in Mission 3.
• Added Fio's death sound (In Metal Slug 2, she uses Eri's)
• The original art for Metal Slug is shown at the end of the game while the credits are rolling, instead of the black screen used in Metal Slug 2.