The concept of the daisho originated with the pairing of a short sword with whatever long sword was being worn during a particular time period. The tachi would be paired with a tantō, and later the katana would be paired with another shorter katana called a chiisagatana. With the advent of the katana, the wakizashi eventually was chosen by samurai as the short sword over the tantō. Kanzan Satō, in his book titled The Japanese Sword, notes that there did not seem to be any particular need for the wakizashi and suggests that the wakizashi may have become more popular than the tantō as the wakizashi was more suited for indoor fighting. He mentions the custom of leaving the katana at the door of a castle or palace when entering while continuing to wear the wakizashi inside.

Daishō may have become popular around the end of the Muromachi period (1336 to 1573) as several early examples date from the late 16th century. An edict in 1629 defining the duties of a samurai required that daishō be worn when on official duty. Wearing daishō was limited to the samurai class in 1683, and became a symbol of their rank Samurai could wear decorative swords in daily life, but the Tokugawa shogunate regulated the appearance of swords for formal attire such as when samurai came to a castle. The daisho for formal attire was limited to the scabbard in solid black, the hilt winding thread and the hilt wrapped with white ray skin.

According to most traditional kenjutsu schools, only one sword of the daisho would have been used in combat. However, in the first half of the 17th century, the famous swordsman Miyamoto Musashi promoted the use of a one-handed grip, which allowed both swords to be used simultaneously. This technique, called nitōken, is a main element of the Niten Ichi-ryū style of swordsmanship that Musashi founded.

During the Meiji period an edict was passed in 1871 abolishing the requirement that daishō be worn by samurai, and in 1876 wearing swords in public by most of Japan's population was banned; thus ended the use of the daishō as the symbol of the samurai. The samurai class was abolished soon after the sword ban.