The Ninja is one of the endgame jobs of Final Fantasy III, alongside the Sage. How it is accessed varies between versions: In the original games, it was awarded with the Elder Staff. In the 3D remake, it is moved to the Earth Crystal.The Ninja first appeared in the original Final Fantasy as the job upgrade for the Thief. The job would go on to be a recurring job throughout the series, with the likes of Edge, Shadow and Yuffie in particular representing it.
In the Famicom version of Final Fantasy III, the Ninja was strongest physical job, having the highest stats and being able to equip any and all equipment. The only job that came close was a maxed out Onion Knight, and even then it was just barely (mainly due to the Ninja's unimpressive Int and Mnd stats along with slightly lower Vit). In particular, the job had access to Shurikens: One-time-use weapons that do major damage.
In the 3D remake, the Ninja was nerfed and thus moved to the Earth Crystal. Compared to the Sage, however, the job was moreso reworked than nerfed: Most of the equipment it could previously access was removed, leaving knives, throwing weapons and Dark Blades. In return, the Ninja gained the Throw command, allowing them to fling any weapon at the enemy. Throw has an impressive power, potentially making the Ninja one of the strongest jobs in the game.
Unlike the Sage, the Pixel Remaster's stat changes to Ninja are more varied: its Phys and Agility were restored to their perfect stats, its vitality isn't as high as the original, but not as low as the remake and the its Int and Mnd are based on the remake, making them slightly higher than the original.
In the 3D and PR versions, the Ninja has access to the famous, recurring command. The Ninja can select an item in the inventory and hurl it at the opponent. The hit chance is near-guarenteed and the damage tends to be in the thousands (A Loki Harp at job level 1, for example, will usually deal somewhere between 2000-4000+ damage) and scales with the job level. The catch is that the item thrown will be removed from the inventory permanently: Meaning that throwing a one-of-a-kind item means that you lose it for good.
The original game had a prototypical form of this in Shurikens. Shurikens return in the remake as the highest damage item (even at job level 1, it should deal 6000+ damage) albeit at the cost of 65,500 gil. Still, this quirk makes the Shurikens extremely useful for the superboss: the Iron Giant.
While the typical defense strategy of employing a Knight is recommended, especially as the Ninja's defense are less than impressive, the Ninja should be in the front lines as an attacker. In a pinch though, they can move to the back and use ranged weapons to attack, although one of those weapons is in Eureka.
The guide also provides charts noting the most and least economical weapons to purchase for use with Throw, as well as the weapons that give a Ninja the most damage for their gill. Interestingly, the Shuriken isn't the least economical weapon (that goes to the Apollo Harp) nor the most damage/gil (of the top 5, it is the worst: The Ashura has the most "bang per buck" with a 0.61 ratio, the Shuriken only having a 0.25 ratio).