The 26-year-old beat off competition from Jack Cork, who came in second and top goalscorer Martin Paterson, who came in third.
Club secretary Bernard Griffin said: "In the closest contest for years, Joe just pipped Jack Cork to the award with Martin Paterson third in the voting.
"Thanks to all members who cast their votes."
Murphy voted Player of the Year
Murphy will be presented with his award at the Official Supporter's Club awards night on Sunday May 4 after the Colchester United game.