Born in Kitagawa-gō, Aki District, Tosa Province (present-day Kitagawa Village, Kochi Prefecture), he joined Takechi Hanpeita's Tosa Loyalist Party and threw himself into the sonnō jōi movement, but was forced to leave his domain after the crackdown. He then worked energetically as a go-between for Choshu and Satsuma domains, and was deeply involved alongside Sakamoto Ryoma in forging the Satcho Alliance of 1866. Where Ryoma organized the Kaientai (naval force), Nakaoka organized and led the Rikuentai (land force); their activities were complementary, and the two are sometimes called the twin pillars of the Bakumatsu Restoration movement. On the night of November 15, 1867, he was attacked with Sakamoto Ryoma by assassins at the Omi-ya inn in Kyoto (the Omi-ya Incident). Ryoma died on the spot, but Nakaoka survived for two days and in his dying moments passed on an account of what had happened. He was twenty-nine. Alongside Ryoma, he is still beloved today as a hero who heralded the dawn of modern Japan.

Sincere and full of initiative, he was a conciliatory activist who sought to build connections between domains with a broad perspective. Though often overshadowed by the charismatic Sakamoto Ryoma, his contribution to realizing the Satcho Alliance was no less than Ryoma's.

His contribution to realizing the Satcho Alliance was directly linked to the achievement of the Meiji Restoration. Beloved alongside Sakamoto Ryoma as a Bakumatsu hero by the people of Kochi Prefecture, the Nakaoka Shintaro Museum in Kitagawa Village preserves his legacy today.