Jordan was born in Danville, Maine to Benjamin and Lydia (Wright) Jordan on October 13, 1822. He was of English descent.
He married Julia M. Clark on January 13, 1847. They had five children:
- Walter Jordan (8 Jun 1848-19 Jan 1854)
- James Clark Jordan (12 Apr 1850-?) married Helen Stevens (four children)
- Julia Maria Jordan (17 Oct 1852-?) married Herbert Dumaresq (one child)
- Eben Dyer Jordan Jr. ( 7 Nov 1857-1916)
- Alice Jordan (12 Apr 1863-1935) married Arthur Wellesley Foster TD DL JP (two children).
- A grandson Arthur Cedric Foster was K.I.A. in WW1.
Jordan died on November 15, 1895.