Consider if want to experience being a ninja or samurai, or just want to visit historical sites. If you want to put on ninja or samurai traditional costume and learn how to throw a shuriken (metal ninja star), popular Japanese tour company H.I.S offers a ninja experience tour in Tokyo. Additionally, Japanese travel agency JTB offers a ninja and samurai experience tour of Tokyo that allows tour participants to take part in a mock samurai battle.
Research ninja and samurai historical sites in Japan. Decide which ones you want to visit. Many tours only explore Tokyo and its surrounding area, so if you are interested in a tour experience of the central-southern region, consider a company like Dragonfly tours, which offers visits to a ninja home with hidden compartments and artifacts and a ninja village in Osaka. Japan Roads Tours also offers visits to preserved samurai villages with an extensive tour of sites in Tokyo and Central Japan.
Create your own side trip. If you're already going to Japan and you want to spend a day or an afternoon enjoying a ninja or samurai experience, contact a tour operator or visit sites on your own. Japanese travel agency H.I.S offers an afternoon ninja cultural experience tour in Tokyo at a ninja-theme restaurant. In Central Japan, you can visit the Ninja Museum to get a great overview of the ninja history and lifestyle.