The 6-10, 252-pound Okafor was the Bobcats' top pick in the 2004 NBA Draft out of Connecticut, shortly after he helped the Huskies win the NCAA title.
Second place in the rookie voting went to Chicago's Ben Gordon, Okafor's teammate at Connecticut. Gordon had won the league's sixth-man award Tuesday.
Okafor was named Rookie of the Month three times, averaging 15.1 points and nearly 11 rebounds per game this season.
"It's an honor to win the Rookie of the Year with such other talented candidates," Okafor said at a news conference. "This is an award that every rookie strives to get and it means a lot to me."
Orlando forward Dwight Howard was third in the rookie voting.