Ellen Gleditsch was born in 1879 in Mandal, Norway. She was the daughter of Petra Birgitte Hansen (1857–1913) and headmaster Karl Kristian Gleditsch (1851–1913). Her siblings included architect Eivind Gleditsch(nl), Adler (1893–1978) who lived with her for the rest of her life following the death of their parents, Liv Gleditsch (1895–1977) who graduated with a degree in chemistry, and civil engineer and geodesist Kristian Gleditsch. The family moved to Trondhjem and then Fredrikshald in 1905. She was the niece of Jens Gran Gleditsch and Kristen Gran Gleditsch, a first cousin of Henry Gleditsch and second cousin of Rolf Juell Gleditsch and Odd Gleditsch, Sr. Her sister in law through Kristian was Nini Haslund Gleditsch (1908–1996).
Although she graduated from high school at the top of her class, the college entrance exams were not available to women at the time. Therefore, she worked as a pharmacy assistant where she was able to work toward a non-academic degree in chemistry and pharmacology in 1902. In 1905 with the support of her mentor Eyvind Bødtker, she passed the university entrance exam, but chose to study in Paris.