Murphy, among the favourites for the Brownlow won by Magpie Dane Swan on Monday night, polled 94 votes to finish in front of teammate Chris Judd (90).
Hawk Sam Mitchell and Western Bulldogs captain Matthew Boyd (87 each) tied for third with Sun Gary Ablett and Swan (both 80) rounding out the top five.
The award saw each senior coach vote on a 5,4,3,2,1 basis after each home and away game.
At the Brownlow Medal count on Monday night, Murphy and Mitchell became the only players in history to poll in 12 matches and not go on to claim the AFL's highest individual honour.
The 24-year-old said he was "thrilled" to be recognised by the coaches after a career-best season.
"This year has definitely been my most consistent," Murphy said.
"I've had a lot of help from a lot of people, the coaches sitting on my table tonight. They've had a big impact on my footy career.
"Hopefully, it's a stepping stone into next year … and that we can play more finals footy in the next couple of years."
AFLCA Player of the Year final tally
Marc Murphy (Carlton) - 94
Chris Judd (Carlton) - 90
Matthew Boyd (Western Bulldogs) - 87
Sam Mitchell (Hawthorn) - 87
Gary Ablett (Gold Coast) - 80
Dane Swan (Collingwood) - 80
Scott Pendlebury (Collingwood) - 79
Scott Thompson (Adelaide) - 74
Daniel Wells (North Melbourne) - 73
Trent Cotchin (Richmond) - 71
