The Harvard Aikido Club began unofficially as a recreation class in 1977 with instructors in Ki Society, until 1980, when the first official Hombu instructor was Glenn Webber. The Club was officially founded by Eugene Taylor, then a Resident Graduate at Harvard Divinity School in Applied Theology and History of Religions, before he received his shodan (first degree black belt) in Aikikai Aikido under Mitsunari Kanai-shihan. The club established a close affiliation with the MIT Aikido Club under Dick Stroud-sensei, a relationship it maintains to this day. In 1981, the Club became an official dojo of the United States Aikido Federation. This was the same year that Kanai-shihan instructed Taylor to prepare for the shodan exam and after successfully passing it in New York under Yoshimitsu Yamada-shihan, Taylor-sensei was designated by Kanai-shihan as the official instructor of the dojo. Taylor-sensei also joined the faculty at Harvard Medical School in psychiatry at that time, becoming the official faculty sponsor of the Club. Eugene Chang-sensei became a co-instructor a few years later.

All classes were originally held in a portion of what is now the Fencing Club on the third floor of the undergraduate gym. When the gym was renovated in 1984, the Club practiced for a year in one of the University squash courts next to Adams House, and then moved back into the undergraduate gym, which by then had been renamed the Malkin Athletic Center. The Club was assigned the two recreation rooms on the third floor, where it meets to this day.

Originally the recreation classes were quite small, but within a few years they swelled at times to 100 new students per year. The mission of these classes was to provide a basic introduction to Aikido. Sometimes these classes were challenging as the number of students was great and the size of the rooms small. However, for a good many curiosity grew into a long term interest, ensuring that the Club classes would remain well-attended once formal instruction in the art got underway each year. Aikido at Harvard became quite popular, due to the unwavering attention of the instructors, a highly favorable evaluation in the Unofficial Guide to Harvard, the high retention rate of women, and the non-violent nature of the art. At one point, the yoga and aikido instructors were taking each other's classes, and their students soon followed. This led to an intense period of interaction and, for almost a two-year period, a cohort of Harvard and Radcliffe undergraduates took yoga and aikido simultaneously.

Currently, the Harvard Aikido Club offers classes three times a week during the school year and closes during the summer and winter vacations. In 2001, the Harvard Aikido Club, with the invaluable help of the MIT Aikido Club, celebrated the promotion of their first "homegrown" shodan, an important achievement for any student and university club. Until 2004, Eugene Taylor-sensei, yondan (fourth degree black belt) and a shidoin in the United States Aikido Federation, served as the Chief Instructor of the Harvard Aikido Club. At the start of the 2005-2006 school year, Taylor-sensei passed on the title of Chief Instructor to Sioux Hall, a godan (fifth degree black belt) and a student of the late-Mitsunari Kanai of New England Aikikai. Hall-sensei is assisted by several yudansha (black belts) and continues the legacy of excellence that Taylor-sensei began so many years ago.

Since one of the fundamental missions of the Club is to enrich the cultural life of students and contribute to their inner development, the Harvard Aikido Club is always seeking to establish exchanges with other cultural groups as well as other martial arts clubs on campus, and welcomes everyone, regardless of his or her background in martial arts.