He was educated in the schools of Middletown, Connecticut and Amherst, Massachusetts[3] and graduated from Yale College in 1833, where he was a member of the Linonian Society.

He studied medicine at the Jefferson Medical College, Philadelphia, receiving his M.D.

Hunt became a prominent physician in Hartford, President of the Connecticut State Medical Society in 1864 and 1865, director and medical visitor of the Connecticut Retreat for the Insane (now called The Institute of Living), and physician to the Asylum for the Deaf and Dumb (now called the American School for the Deaf).

Together, Ebenezer and Mary were the parents of four children, including:[4] Hunt died in Hartford on May 2, 1889.

The E. K. Hunt Chair (i.e., Professorship) of Anatomy at Yale University is named after him.