Merz was born in Niagara Falls, New York, on January 24, 1959. His family moved to Gladwyne, Pennsylvania, where he graduated from Harriton High School in 1977. Merz studied chemistry at the undergraduate level at Washington College and where he graduated in 1981. In 1985, he received his Ph.D. from the University of Texas at Austin under the supervision of M. J. S. Dewar. After postdoctoral appointments with Roald Hoffmann from 1986 to 1987 and Peter Kollman from 1987 to 1989, he started his academic career at the Pennsylvania State University.