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She was the astronomy instructor to several generations of astronomers at the turn of the century, including Annie Jump Cannon. She originally went to Wellesley College as its first professor of physics. After observing the undergraduate physics labs at MIT while she attended classes there, she established the physics labs at Wellesley. Hers was only the second undergraduate physics lab to be started in the country (the first was at MIT).
While at MIT she met a physics professor named Edward Pickering. He left MIT to become the director of the Harvard College Observatory in 1877. He invited Whiting to observe some of the new techniques which were being applied to astronomy, in particular, spectroscopy. Inspired by this, she introduced the teaching of astronomy at Wellesley in 1880. She was the first director of the Wellesley College Observatory after helping to establish it in 1900.