Nathan first played shortstop for the then Division III Stony Brook Patriots (now Division I and called the Seawolves) at Stony Brook University on Long Island, New York. He also played for the Fairfield Stallions in the New England Collegiate Baseball League in 1994. Nathan became a two-time Academic All-American and graduated as a member of the Golden Key International Honour Society. During his tenure at Stony Brook, professional baseball scouts began to notice his good arm and pitcher's body. Senk arranged for a game in front of scouts, but on a day that "literally someone from every organization" came to watch him pitch, the game was rained out. The scouts had to settle for watching Nathan in a throwing session. He was drafted in the sixth round (159th overall) of the amateur draft by the San Francisco Giants in 1995 and signed the next day, June 2.