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Born in 1867 in Onsen District, Iyo Province (today Matsuyama, Ehime), as the eldest son of the Matsuyama-domain samurai Masaoka Tsunenao; his given name was Tsunenori. He lost his father at five and received strict Chinese-classics training from his maternal grandfather Ohara Kanzan. He went up to Tokyo in 1883, entered the Philosophy Department of Tokyo Imperial University in 1890 (later transferring to Japanese literature), left in 1892 and joined the newspaper 'Nippon.' His 1893 essay 'Basho Zatsudan,' published at 26, criticized the then-deified Matsuo Basho as 'eight or nine of every ten Basho haiku are inferior,' shocking the traditional haiku world and igniting the haiku reform movement. He set 'shasei' (sketching from life) as his theoretical pillar, advocating an objective description method that copies what is seen as it is. In 1898 he led the magazine 'Hototogisu' and trained disciples such as Takahama Kyoshi and Kawahigashi Hekigodo. In tanka too, in 1898 with 'Letters to the Tanka Poets' he denied the 'Kokin Wakashu' and exalted the 'Manyoshu,' presiding over the Negishi Tanka Society. In 1895 he traveled to the Liaodong Peninsula as a Sino-Japanese War correspondent, but on the way home suffered a major hemoptysis on board ship; from then he suffered from spinal caries and a bedridden life began. Battling intense pain, he wrote his late masterpiece essays 'Byosho Rokushaku,' 'Gyoga Manroku,' and 'Bokuju Itteki,' and on September 19, 1902, died at the Shikian in Negishi, Tokyo, at 34. He kept his brush moving until the day before his death.

He burned with the spirit of reform and had an iron will that could criticize tradition without fear. Despite seven years of bedridden life battling intense pain, he kept his brush moving until his very last day — an awesome mental strength. He also had a sense of humor, enjoying the wordplay of translating 'baseball' as 'noboru' from his name, and translated baseball terms such as 'batter,' 'runner,' and 'walk' (inducted into the Baseball Hall of Fame in 2002).

The greatest contributor to the modernization of haiku and tanka. The 'Hototogisu' he founded continues to this day and became the matrix of modern haiku circles. His theory of 'sketching from life' became the mainstream through his disciple Takahama Kyoshi, and Natsume Soseki too opened his eyes to haiku and the novel under Shiki's influence (Soseki and Shiki were close friends from the same Tokyo University year). For his translation and popularization of baseball terms he was inducted into the Baseball Hall of Fame in 2002. His native Matsuyama proclaims itself 'City of Haiku.' The Shikian in Negishi, Tokyo, is preserved as a memorial of his last seven years.