Anthony Czarnik attended the University of Wisconsin and received his B.S. in Biochemistry in 1977. He then studied with Nelson J. Leonard at the University of Illinois at Urbana–Champaign and earned an M.S. in biochemistry in 1980 and a Ph.D. in chemistry in 1981 with a thesis, "Chemical studies on nucleic acid analogues." He then studied with Ronald Breslow at Columbia University (1981–1983) as an NIH Postdoctoral Fellow.