Ueshiba was born on June 27, 1921, in the city of Ayabe, Kyoto Prefecture, Japan. He was the third son and fourth child of Morihei Ueshiba and Hatsu Ueshiba (née Itokawa). Ueshiba began training under his father around 1937.

In 1942, while he was still studying at Waseda University, Morihei Ueshiba (who was retiring to Iwama) appointed him the head of the Kobukan Dojo in Shinjuku, Tokyo. He saved the dojo from fire bombing several times during the World War II. Ueshiba graduated with a degree in economics in 1946.

Speaking about the period just after World War II, Moriteru Ueshiba said, "there was not yet much activity at the Hombu Dojo. For a time my father [Kisshomaru Ueshiba] was actually in Iwama instead ... starting around 1949, he worked for about seven years at a company called Osaka Shoji. He had no other choice. Even if you have a dojo, you can't make a living if nobody is coming to train, which was largely the case after the war. So, he took a job as an ordinary company employee during the day and taught only in the mornings and evenings."

Beginning in 1948, Ueshiba oversaw the development of the Aikikai Honbu organization (and eventually the tearing down of the Kobukan Dojo in 1967 to construct the Aikikai headquarters).

After Morihei Ueshiba's death in 1969, Kisshomaru Ueshiba took on the mantle of Doshu (hereditary head). In 1995, Ueshiba received the Zui Hosho Medal from the Japanese government. By 1998, Ueshiba's health had declined and this necessitated visits to hospital.

Ueshiba died around 5:30 PM on January 4, 1999, in a Tokyo hospital. The cause of death was respiratory failure. As his father was the first Doshu, he was the second Doshu, and after his death, his son Moriteru Ueshiba became the third Doshu, following the iemoto system.