Zimmermann, 26, was eligible for arbitration for the first time this offseason. His agent had asked for $5.8 million for the 2013 season, while the Nationals had countered with $4.6 million.
Terms of the deal are not yet known.
The two sides had an arbitration hearing scheduled for Feb. 19, but today's deal means an arbiter won't be needed.
Zimmermann went 12-8 with a 2.94 ERA over 195 2/3 innings last season. He finished seventh in the National League in ERA and fifth in WAR (Wins Against Replacement).
Up to this point, Zimmermann and the Nationals have not been in discussions on a long-term deal, first choosing to reach terms for this upcoming season and get this process out of the way. Zimmermann has said he would be open to the idea of a long-term extension, however, and now we'll have to see whether Zimmermann's side and general manager Mike Rizzo begin such talks.
The Nationals have now reached terms with all seven of their arbitration-eligible players.
Update: Zimmermann will earn $5.35 million this season, a source confirmed.