Cubillos-Ruiz received a bachelor’s degree in microbiology from Universidad de los Andes Bogota, Colombia) in 2004, and obtained his Ph.D. in tumor immunology from Dartmouth Medical School in 2010 under the mentorship of Dr. Jose Conejo-Garcia. Cubillos-Ruiz then pursued his postdoctoral training at Harvard University and Weill Cornell Medicine in the laboratory of Dr. Laurie H. Glimcher.