Popular belief is that the nunchaku was originally a short Southeast Asian flail used to thresh rice or soybeans (that is, separate the grain from the husk). It is possible that it was developed in response to the moratorium on edged weaponry under the Satsuma daimyo after invading Okinawa in the 17th century, and that the weapon was most likely conceived and used exclusively for that end, as the configuration of actual flails and bits are unwieldy for use as a weapon. Also, peasant farmers were forbidden conventional weaponry such as arrows or blades so they improvised using only what they had available, farm tools such as the sickle. The modern weapon would be an effective flail.

Some sources say that the first Song Emperor was in battle when an enemy general cut the end off of his staff. Instead of using a different staff, he connected the two pieces with a short section of iron chain, creating a weapon known as "sweeper". At the time, it was not illegal to carry a weapon, but it was inconvenient to carry a sweeper because it was a long stick with a loose section, so some people shortened the staff section so that the weapon could be tucked in a belt. This was called a "small sweeper", later renamed the nunchaku.

Another popular theory is that the nunchaku originated from China in the Song Dynasty. It was named "da pan long gun", meaning great coiled dragon stick. The weapon is composed of one long stick and a short stick connected by horse hair. It was commonly used in wars against cavalry to trap horse legs. The weapon eventually evolved into a short range weapon as seen in present day nunchaku.

A nunchaku is two sections of wood connected by a cord or chain, though variants may include additional sections of wood and chain. Chinese nunchaku tend to be rounded, whereas the Okinawan version has an octagonal cross-section (allowing one edge of the nunchaku to make contact on the target increasing the damage inflicted).

The Nunchaku-Do sport, governed by the World Nunchaku Association, promotes black and yellow Styrofoam nunchaku. Unlike readily available plastic training nunchaku, the ones they promote are properly balanced.