In 1866, Stimson was married to Candace Thurber Wheeler (1845–1876), the daughter of Thomas Mason Wheeler (1818-1895) and Candace Thurber Wheeler (1827–1923).
They had met in Trenton, New Jersey.
Wheeler was described as a "beautiful creature, endowed with all the graces and accomplishments — a rare musician and vocalist, and of a nature as lovely as her person."
His biographer wrote that "his devotion to her began with their first meeting, and lasted as long as his life.
It was the mainspring of much of the tenderness and compassion that marked his relation to humanity."
 Lewis and Candace were the parents of:
Henry Lewis Stimson (1867–1950), Secretary of State in Herbert Hoover's Administration as well as Secretary of War in the William Howard Taft Administration and the Franklin Delano Roosevelt Administration.

Candace C. Stimson (1869–1944), who helped administer the anti-tetanus serum around Europe during World War I with her father.

In a memorial written for Stimson after his death, Edward Lawrence Keyes (1843–1924) wrote about Stimson and his wife:
"Dr. Stimson impressed me as a man of very deep feeling which he kept under perfect restraint.
He once drove me to Woodlawn Cemetery where he looked over his wife's grave.
He spoke briefly but feelingly.
I asked him how he ever survived such a loss.
He replied, 'By years of constant, grinding work.'."

Stimson died on September 17, 1917 at Shinnecock Hills, New York.
In 1866, Stimson was married to Candace Thurber Wheeler (1845–1876), the daughter of Thomas Mason Wheeler (1818-1895) and Candace Thurber Wheeler (1827–1923). They had met in Trenton, New Jersey. Wheeler was described as a "beautiful creature, endowed with all the graces and accomplishments — a rare musician and vocalist, and of a nature as lovely as her person." His biographer wrote that "his devotion to her began with their first meeting, and lasted as long as his life. It was the mainspring of much of the tenderness and compassion that marked his relation to humanity."  Lewis and Candace were the parents of:
Henry Lewis Stimson (1867–1950), Secretary of State in Herbert Hoover's Administration as well as Secretary of War in the William Howard Taft Administration and the Franklin Delano Roosevelt Administration. 
Candace C. Stimson (1869–1944), who helped administer the anti-tetanus serum around Europe during World War I with her father.
In a memorial written for Stimson after his death, Edward Lawrence Keyes (1843–1924) wrote about Stimson and his wife:
"Dr. Stimson impressed me as a man of very deep feeling which he kept under perfect restraint. He once drove me to Woodlawn Cemetery where he looked over his wife's grave. He spoke briefly but feelingly. I asked him how he ever survived such a loss. He replied, 'By years of constant, grinding work.'."
Stimson died on September 17, 1917 at Shinnecock Hills, New York.
Lewis Atterbury Stimson