Henry C. Whittington was born in Baltimore, Maryland. He was the son of Benjamin Whittington and his second wife, Elizabeth Cowman. His paternal grandparents were Thomas Whittington and Wilhelmina Powell, whose plantation "Maidstone" was in Anne Arundel County (now Calvert County), Maryland. The old house still stands and is listed on the National Register.

Henry's mother died when he was young and he was raised under the care of a black "mammy" on his uncle's plantation. He married Margaret Boyer Richardson in 1834 in Ohio. The couple had 11 children: Benjamin, Sarah, Mary, Sophia, John, Eleanor ("Ellen"), Martha, Julia, Margaret Emily ("Emma"), Amanda, and Susan.

In 1852 they sold their farm in Summerfield, Ohio and moved to Iowa by boat, going down the Ohio and up the Mississippi Rivers and landing in Keokuk. They carried the gold coins from the sale of the farm sewn in their clothing for safety from robbers. For two years, the family lived on a farm about five miles from Farmington, then moved to Banner Valley near Ely where they purchased a farm that became the family home for many years.

In 1861 their son, John Whittington, joined the Union army. He was killed by a rebel sharpshooter while on sentry duty near Grand Gulf, below Vicksburg and was buried on a bluff overlooking the Mississippi River.

In 1862-1863 the family moved to Iowa City and lived for a time in the north part of the city on property now part of a cemetery.

Henry's wife, Margaret, died March 24, 1875 and is buried in Solon, Iowa. She had been a semi-invalid for many years due to a severe case of typhoid fever. Following her death, Henry married a widow named Harriet Lingo and moved to Mankato, Kansas with her to live. He died of Brights disease. His grandson, Charles Keyes remembered him as "barrel chested."