Ebara was born in Edo as the son of a lesser retainer of the Tokugawa Shogunate, but was an exceptionally talented scholar and selected for the Shogunal military academy based on his performance at the terakoya temple schools.
Following his combat service at the Battle of Toba-Fushimi during the Boshin War of the Meiji Restoration, he visited the United States. On his return to Japan, he moved to Shizuoka prefecture to be near the former Shogun Tokugawa Yoshinobu and assisted in establishing the Numazu Military Academy and Numazu Junior High School. Converting to Christianity in 1877, he was responsible for starting the Numazu Church. Later, Ebara served as chairman of the Tokyo YMCA.
In 1890, Ebara was elected in the Japanese general election, 1890 to the House of Representatives in the Diet of Japan and served as a member of the Liberal Party, the Kenseikai, and the Rikken Seiyūkai. In 1912, he was appointed to the House of Peers. He was sent to the United States to try to ease tension over California’s Alien Land Law of 1913.
Ebara is also remembered as the founder of Azabu High School (then a middle school).