Sophia Eckerson was born around 1880 (her exact date of birth is unknown) in Old Tappan, New Jersey to Albert Bogert Eckerson and Ann Hennion Eckerson. After graduating from secondary school, Eckerson did not immediately go to university and instead helped her brothers in college. By 1901, however, she had enrolled in Smith College in Massachusetts where she was inspired by William Francis Ganong to study and pursue a career in botany and plant physiology.