He married as his first wife, on August 10, 1872, at Abington, Plymouth County, Massachusetts, Charlotte Elizabeth Noyes, born on August 10, 1850, at Abington, Massachusetts, the daughter of Lewis Ellingwood Noyes and Lucy A. Briggs. She was an 1870 graduate of Mount Holyoke College and was a school teacher before her marriage in 1872. She was a descendant of Dr. Samuel Fuller, a passenger on the Mayflower and one of the Separatist settlers of the Plymouth Colony in Massachusetts. They were the parents of a son, Henry Walker Starbuck (1874–1948). This couple later divorced.
