Eppes was born at Eppington, Chesterfield County, Virginia the only son and youngest of six children of Francis Eppes and Elizabeth (née Wayles) on April 19, 1773. He attended the University of Pennsylvania at Philadelphia and graduated from Hampden-Sydney College in Virginia in 1786. He studied law and was admitted to the bar in 1794 and commenced practice in Richmond, Virginia.

He married his cousin Maria (known to her family as Polly), the daughter of Thomas Jefferson, October 13, 1797 at Jefferson's home of Monticello, Charlottesville, Albemarle, Virginia. Amongst the wedding presents received from Jefferson was the 14-year-old slave Betsy Hemmings (who may have been Jefferson's illegitimate daughter). Eppes and Maria had three children: a daughter born December 31, 1799 who lived only weeks; a son Francis (September 20, 1801 - May 30, 1881) and Martha (February 20, 1804-July 1807). His wife Maria died just two months after bearing Martha, on April 17, 1804 at her father's home. Eppes moved to a new plantation called Milbrook where Betsy Hemmings is recorded as being the nurse of his son Francis. When Betsy had a daughter by Eppes the child was named Frances.

In 1809 Eppes married nineteen-year-old Martha Jones from North Carolina; she was known as Patsy. They had their first child in 1810 and the last in 1820.

Eppe was a member of the Virginia House of Delegates from 1801 to 1803 and on March 4, 1803 he was elected as a Democratic Republican to the Eighth United States Congress and the next three succeeding Congresses. He chaired the Ways and Means Committee for the Eleventh Congress but failed to be elected to the Twelfth. and spent two years planting at Milbrook. He was elected to the Thirteenth Congress (March 4, 1813-March 3, 1815) and chaired the Committee on Ways and Means again. After losing the election to the Fourteenth Congress he was elected to the United States Senate and served from March 4, 1817, until December 4, 1819, when he resigned because of ill health. He chaired the Committee on Finance for the Fifteenth Congress.

Eppes retired to his estate, ‘Millbrook’, in Buckingham County, Virginia, where he died September 13, 1823 and was interred in the private cemetery of the Eppes family at Millbrook, near Curdsville, Virginia. When Betsy Hemmings died in 1857 she was buried next to Eppes' grave with an elaborate stone. Patsy Eppes died at Millbrook in 1862 and was buried at her daughter's home in nearby Chellowe instead of beside her husband at Millbrook. Anecdotal evidence suggests that Patsy Eppes would not be buried near her husband's mistress, Betsy Hemmings.

A portrait of Eppes hangs in the dining room of Weston Manor house in Hopewell, Virginia. The plantation was a wedding gift to his cousin Christian Eppes and William Gilliam.