Nagakura's father spelled the family name with the "naga" meaning "long", but Nagakura later spelled it with the "naga" meaning "eternity". At eight, Nagakura entered Okada Juusuke Toshisada's Shintō Munen-ryū dojo; at age eighteen he reached mokuroku (6th dan), and received the menkyo kaiden certification. At age nineteen he left the service of the Matsumae clan in order to travel and improve his technique. He spent some time at Yurimoto Shuuzou's Shintou Munen Ryu dojo. Nagakura also spent time at Tsubouchi Shume's Shingyoto Ryu dojo, where he met Shimada Kai, the future vice-captain of the Shinsengumi 2nd unit. Around 1861, he started "taking his meals" at Kondou Isami's Shieikan.
Nagakura became a fukuchou jokin (assistant vice commander) in 1863, then became the captain of the 2nd unit in 1865. Together with the rest of the Shinsengumi, he became a hatamoto in 1867.
Right after the Battle of Kōshū in April 1868, Nagukura left the old Shinsengumi with Harada Sanosuke and formed the Seiheitai (after disagreements with long-time comrades, Kondo and Hijikata.)
Later, Nagakura held requiems for his past comrades' souls. Some four years before his death, he gave an oral background of the Shinsengumi to a journalist for a newspaper. It is believed that since the reports were given half a century after the events, the accounts are more for pleasing crowds than a faithful record.
Nagakura did, however, keep memoirs that can constite first hand to the bloody lifetime of the Shinsengumi. These memoirs were lost for decades before being found and published in book form in 1998.
For example, Nagakura is featured in Peacemaker Kurogane (anime/manga), Kaze Hikaru (manga), Getsumei Seiki (manga), 2004 NHK Taiga drama series Shinsengumi!, Shinsengumi Gunrou-den (video game series), and Bakumatsu Renka Shinsengumi (video game series.)