Scherzer breezed past Los Angeles Dodgers ace Clayton Kershaw and Nationals teammate Stephen Strasburg, drawing 27 of the 30 first-place votes in balloting by members of the Baseball Writers' Association of America.
"Yes!'' Scherzer shouted, thrusting his arms up when the honor was announced on MLB Network.
The 33-year-old righty Scherzer earned the NL honor last year with Washington and the 2013 American League prize with Detroit. He became the 10th pitcher with at least three Cy Youngs.
Scherzer led the National League with 268 strikeouts and ranked second in ERA (2.51) and fourth in wins (16) for the NL East champion Nationals.
Kershaw has already won three NL Cy Youngs, and was the most recent pitcher to win back-to-back. He was 18-4 with a league-best 2.31 ERA and 202 strikeouts.
Scherzer, along with AL Cy Young Award winner Corey Kluber, had rough outings in the playoffs. Voting for the awards was completed before the postseason began.
The final BBWAA honors will come Thursday when the MVP awards are announced in the AL and NL.