The simple answer is no. The more detailed answer is no with a few caveats.

Throughout the medieval period, people were employed as spies and agents, gathering information on enemy armies, castles, settlements, and occasionally conducting acts of sabotage and assassination.

These agents had various terms including Ninja and Shinobi. The earliest suggestions of ninja activity dates back to the 12th century, though they were far more common in the centuries of warfare to follow.

Stephen Tunebull notes that their roles were often covert, relying on blending in and not drawing attention. Far more practical than wearing black pyjamas and a balaclava is dressing normally and not drawing attention to oneself.

The ninja are often associated with the clans of the Iga province, which was a hiring ground for these agents. However, there is no evidence of anything today related with the ninja. Most were illiterate mercenaries who operated outside the common societal bounds of “honour”. They were spies, agents, thugs, and did operate with stealth in much the same was as spies anywhere else. However, the concept of mystical arts, secret martial abilities and weapons, and most things today associated with the ninja was a Meiji era fantasy from the 19th century.

The Bansenshukai is a ninja manual from Iga dated to 1676. It comprises chapters on military philosophy and leadership, infiltration techniques, and suggests a codified thinking towards the ninja role. However, much of it is based on 17th century Chinese military philosophy, and bears little resemblance to the Hollywood image of ninja today. Instead, it was written for the Tokugawa Shogunate to preserve the military knowledge and experience acquired from centuries of constant warfare, so it need not necessarily be associated with the ninja specifically, and was written 76 years are warfare (and the common use of ninja) had ended, the country essentially finding a stable peace in 1600.

In essence, we can allow that ninja existed, and even underwent some formal and codified training, most notably centralised around the Iga province during they Sengoku Jidai. We can even allow that they conducted covert infiltration and sometimes assassination, but they were also largely made up of illiterate mercenaries and common thugs who needed work.

To what extent we can ascribe them mystical codes, ancient clans with mystical knowledge, or even ninja stars, straight swords, and black pyjamas is just too limited by the information available to us. It’s clear ninja existed. It is very unlikely that they scaled castle walls in black pyjamas armed with ninja stars and smoke bombs as a matter of course. We can allow that some talented and brave ninja did this on occasion, but there is no evidence to suggest that this approach existed in a codified and established way, or that it defined the ninja.