Paytan was born and raised in Israel. As an undergraduate, Paytan encountered geochemistry which she likens to a big complex puzzle. Paytan obtained undergraduate degrees in geology and biology (1985) and an M.S. in Earth Sciences Oceanography (1989) from Hebrew University of Jerusalem. Paytan's Ph.D. is from Scripps Institution of Oceanography (1996) where she worked with Miriam Kastner on using barite as a recorder of ocean chemistry. After postdoctoral work at University of California, San Diego she moved to the Department of Geological and Environmental Sciences at Stanford, and then onto a position at University of California, Santa Cruz.