As no other country in the Western Hemisphere, homeopathy consolidated as a medical science during the first two decades of the 20th century in Mexico. But what type of science homeopathy was? Three schools emerged as the providers of medical training in the city after the revolution (1910-1917), the National School of Medicine, the National School of Homeopathic Medicine, and the Free School of Homeopathy. These schools’ academic staff engaged in philosophical discussions explaining the relationship between medical science and homeopathy in the curriculum. The works of Fernando Ocaranza, David Cruz, and Higinio Pérez offer a set of views on the body, disease, and medicine that went from total rejection of alternative views such as homeopathy to total integration of science with homeopathy. Ocaranza used the new philosophical medicine of Claude Bernard to discredit the metaphysical explanations of bodily functions proposed by homeopathy. In the same line but emphasizing the importance of homeopathy, David Cruz proposed to use the mechanism of vaccination to explain the basis of homeopathy. Based on evolutionary, biological, physical and physiological arguments, Pérez discredited modern approaches to medicine that removed the human being as the center of all medical inquiries. He placed homeopathy as a medical science that explained how physical forces kept the natural world and the human body in balance. This paper examines their philosophical papers and places them in the context of reforms during and after the revolution that sought to continue the professionalizing and secularizing efforts of the Porfiriato (1884-1910).