Achinstein has taught for many years at Johns Hopkins University, where he is currently Professor of Philosophy. In Spring 2009, Achinstein began teaching at Yeshiva University as the Jay and Jeanie Schottenstein University Professor of Philosophy and is the founder and director of the Center for History and Philosophy of Science of Yeshiva University, New York. He returned to Johns Hopkins in Spring 2011. He has held Guggenheim, NEH, and NSF fellowships, and has served as a visiting professor at MIT, Stanford, and the Hebrew University of Jerusalem.