In 1975, Draper's house, known as the Henry Draper Observatory, in Hastings was designated a National Historic Landmark.
In 1976, New York University founded the John W. Draper Interdisciplinary Master's Program in Humanities and Social Thought (Draper Program) in honor of his lifelong commitment to interdisciplinary study.
In 2001, Draper and the founding of the American Chemical Society were designated a National Historic Chemical Landmark at New York University.