Florida outfielder Chris Coghlan won the award, although he was not on seven of the 32 ballots cast by two writers from each league city. Philadelphia pitcher J.A. Happ was the only player named on all ballots, and he placed second, totaling 94 points. Coghlan totaled 105 points.
Former Cubs infielder Casey McGehee, who batted .301 with 16 homers and 66 RBIs for the Milwaukee Brewers, also received a first-place vote, finishing fifth in the balloting with 18 points.
Wells, a converted catcher who went 12-10 in 27 starts for the Cubs, received one second-place vote. The right-hander's 12 wins and 165 1/3 innings were the most for a Cubs rookie since Kerry Wood won 13 and totaled 166 2/3 innings in 1998.
Wells, 27, led all National League rookie pitchers in starts and ranked second in wins and innings pitched, but he downplayed any talk about the award all season. Cubs manager Lou Piniella called the young pitcher the biggest surprise of 2009.
"He took hold and pitched exceedingly well, and he's been very consistent the whole summer," Piniella said after Wells last start on Oct. 3, when he threw seven shutout innings against Arizona. "The good thing about it is he's gotten the chance to pitch all the way through September. Next year, you've got a starter who's pitched that extra month. We look forward to Randy being in our rotation next year."
Cubs catcher Geovany Soto won the NL Rookie of the Year Award in 2008.
Carrie Muskat is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.