In June of 1975, while in Japan, he met and began training under Masaaki Hatsumi, the founder of the Bujinkan martial arts organization. In 1993, Hayes was awarded the judan (tenth degree black belt) degree from Hatsumi. In 2006 however, George Ohashi, administrator of the Bujinnkan Honbu Dojo in Japan, was ordered by Masaaki Hatsumi to remove Stephen Hayes' name from the board of recognized judans of the Bujinkan saying that Hayes' own conduct had removed him from the Bujinkan.

Hayes returned to the United States with his wife Rumiko in late 1980 when his Japan residency visa ran out, and began teaching and authoring numerous books and magazine articles. There is some evidence that he visited and taught in the United States on ninjutsu as early as 1976. In 1997, he founded the martial art of To-Shin Do, an art based in his experience of bud? taijutsu; his SHK (Stephen K. Hayes) Quest network now spans 18 schools across North America and Europe.

Hayes has worked as an actor in the 1980 TV miniseries Shogun and in 2004 was featured in television program Unsolved History regarding ninja and their practices. In 1985 he was entered into the Black Belt magazine's Hall of Fame as Instructor of the Year. He was again featured on the cover of Black Belt in the March 2007 issue; which contains a chapter from his book Ninja Vol 6, Secret Scrolls of the Warrior Sage. the magazine’s opening editorial as well focuses on Hayes, describing him as "one of the 10 most influential living martial artists in the world".

Hayes is also an ordained practitioner of esoteric Tendai mikkyo Buddhism. He apprenticed beneath Clark Jikai Choffy, an ordained Tendai priest and personal disciple of Archbishop Jion Haba of the Tokyo Reisho-in Tendai temple. He received empowerments and teachings from Rev. Choffy, received transmission in the Homan-Ryu school of Tendai esoteric Buddhism, and in 1991 he received Tokudo priesthood ordination in Tendai Buddhism from Rev. Choffy. In the 1990s, Hayes regularly served as personal protection escort and security advisor for 1989 Nobel Peace Prize winner, Tenzin Gyatso, the 14th Dalai Lama of Tibet. Hayes has also founded a Buddhist Order based on his teachings and experiences with Tibetan Buddhism and Tendai, called the Blue Lotus Assembly.

Hayes now lives and works in Dayton, Ohio.

His works include the non-fiction books Ninja: Legacy of the Night Warrior (Black Belt Communications, 1984), The Mystic Arts of the Ninja: Hynotism, Invisibility, and Weaponry (Contemporary Books, 1985), The Ancient Art of Ninja Warfare: Combat, Espionage, and Traditions (Contemporary Books, 1988), Lore of the Shinobi Warrior (Black Belt Communications, 1989), The Ninja and their Secret Fighting Art (Tuttle Publishing, 1990), 'Modern Hand to Hand Combat: Ancient Samurai Techniques on the Battlefield and in the Street (Periplus Edition, 2010), and the novel Tulku, a Tale of Modern Ninja (Contemporary Books, 1985).