The Nazi movement, heavily rooted in eugenics, caused the persecution and exile of hundreds of neuroscientists. Additionally, eugenic research took place in Nazi Germany with the motivation of improving the so-called "German race" through elimination of hereditary neurological diseases. With the advent of illegal killing of neuropsychiatric patients after World War II started, those patients could be used unethically as research subjects. Thus, neuroscience was at the heart of immoral and unethical activities in Nazi Germany from 1933 to 1945. The Rockefeller Foundation (RF) supported at least twenty exiled academic neuroscientists who either had prior RF support, or who showed "merit" to justify their being awarded limited funds to restart their careers abroad. The RF also supported eugenic neuroscientific research in Nazi Germany (and Denmark) despite escalating racial persecution in pre-war Germany. Some RF funds went to an institute which was also funded by the elite Nazi paramilitary group, the SS. And, an initially RF-funded project, a monkey farm in Würzburg, was used in unethical experiments to prove the cause of multiple sclerosis (MS) with subjects targeted for killing. Overall, the RF walked a fine line between supporting some victims of Nazi persecution, while ironically continuing to fund some neuroscientific research that could be linked to their persecution in the first place, or to destruction of neuropsychiatric patients. While supporting academic refugees was laudable, there was an undercurrent of supporting "best science" without regard for the ethical implications, from which current neuroscientists and others can learn valuable lessons.