Zimmermann was rated the Nationals' best prospect going into the 2009 MLB season, according to Baseball America. In 2009, Zimmermann made the Nationals' roster as the fifth starter; however, the Nationals did not need him in the rotation until mid-April, so Zimmermann opened the season with the Triple-A Syracuse Chiefs. Zimmermann's contract was purchased on April 20, 2009, and he made his major league debut that night, after a two-plus hour rain delay, against the Atlanta Braves. He pitched six innings, allowing two runs on six hits, with three strikeouts and a walk, earning the victory.
Zimmermann experienced elbow pain, and in July landed on the disabled list. After attempted rehab, in August 2009 Zimmermann was diagnosed with a torn ulnar collateral ligament and underwent Tommy John surgery, expecting to miss 18 months. He finished his rookie season of 2009 going 3–5 with a 4.63 ERA in 16 starts.