- Jun 2 Johannes Elias Feisser, Dutch theologist and founder of 1st Dutch baptist church, dies at 59
- Jun 2 Ner Alexander Middleswarth, American politician, dies at 81
- Jun 3 Okada Izō, Japanese samurai (b. 1838)
- Jun 6 William Quantrill, American guerrilla leader in the Confederate Army who led Quantrill's Raiders in the Lawrence Massacre, dies of wounds at 27
- Jun 8 Joseph Paxton, English architect, gardener and MP (Crystal Palace), dies at 61
- Jun 10 Lydia Sigourney (née Huntley), American poet and writer (How to Be Happy; Letter of Life), known as "the Sweet Singer of Hartford", dies at 73
- Jun 13 Cleaveland J Campbell, Union brigadier general, dies at about 29
- Jun 15 Edmun Ruffin, US secessionist/writer, commits suicide
- Jun 15 Jakob Zeugheer, Swiss composer, dies at 61
- Jun 21 Frances Adeline Seward, American First Lady of New York (1839-42) and wife of US Secretary of State William H. Seward, dies of a heart attack at 59
- Jun 23 Samuel Francis DuPont, American Rear Admiral (Union Navy), dies at 61
Assassination
Drug Overdose
Gunshot Wound
Murder
Plane Crash
Suicide