Klumpke was born in San Francisco, California, the daughter of Dorothea Mathilda Tolle, from New York, and John Gerard Klumpke, a businessman. Her older sister, Anna Elizabeth Klumpke, had an infection in her leg that left her with a disability. Their mother took the family to Europe for eighteen months to find physicians for Anna, leaving their father behind in San Francisco. Klumpke says her parents grew apart in her mother's absence, but a 1906 newspaper article implies that John Klumpke had an affair that ended their marriage.
