Up to this era, the Ninja is the best counter to the Rocket Troop, due to their Rapid Deployment allowing them to get the first hit, as well as the Ninja's Stealth making them immune to the Rocket Troop.

If your boost is absurdly high, Ninjas do prove somewhat strong against them as long as they are eliminated quickly. After the Ninjas attack, the Warrior Monk can easily finish the Ninja in two hits, even if they are hidden. The Ninja is generally weak against the Warrior Monk, owing to their massive Dug In and class bonus against the Ninja.

In most cases, you should not use Ninjas to counter Ninjas. If the battlefield is rather forested, this match-up may go sideways depending on who has the higher ground of Stealth. Ninjas can be used to counter Ninjas provided you have yours in greater number to maximize your first initial strike, and eliminate Ninjas before they can do anything. In the Space Ages and beyond, however, the loss of Forests and great statistical increase of all other units of higher eras will eventually make the Ninja retire. In fact, their Stealth only proves most useful against artillery units, as they have the lowest movement, whilst many other units can easily reach the Ninja on the next turn. Their Stealth ability is also somewhat useless, as they do not retaliate, and their range is generally not long enough to make it useful. They do have drawbacks against its fast and heavy unit counters, as well as units with defensive capabilities, however, and they are generally ineffective against them, particularly with their strong defensive capabilities (such as the Ronin Bot's Force Field ability), and they are not very strong against them, despite being able to attack first. The Ninja, like any Rapid Deployment unit, should be used as full armies of 8 to maximize its fast initial first strike.

Forge of empires virtual future troops