At University of California, Irvine, his academic appointments include University Professor and Donald Bren Professor of Biological Sciences, Ecology & Evolutionary Biology (School of Biological Sciences), Professor of Philosophy, (School of Humanities), and Professor of Logic and the Philosophy of Science (School of Social Sciences).
Ныне Франсиско Айала работает в Калифорнийском университете в Ирвайне, занимая должности профессора биологии, экологии и эволюционной биологии (School of Biological Sciences), профессора философии (School of Humanities), профессора логики и философии науки (School of Social Sciences).