[3] Palmer was born to a farming family in Branford, Connecticut on August 29, 1862,[4] and completed a bachelor's degree at Vassar College in 1887.

At Yale, she took two classes in astronomy with Maria Mitchell, although her graduation address concerned Greek tragedy.

[5] Her 1894 doctorate was from the mathematics department at Yale, but its subject was astronomy, as it concerned the calculation of the orbit of a comet C/1847 T1 discovered in 1847 by Maria Mitchell.

Palmer's thesis noted that the comets she chose to study were chosen partially because they had been discovered by women.

[2] During this period, Palmer also determined the orbits of three other comets, and collected a large set of observations of the moons of Jupiter.