The French Athletics Federation (FFA) announced the win on Monday.
21-year-old Lemaitre won gold in the 100 metre, 200 metre and 4 x 100 metre relay at the 2010 European Championships in Barcelona.
In 2011 he became the first caucasian to break the 10-second barrier in an officially timed 100 metre race when he achieved a time of 9.92 seconds.
The award is voted by readers of Athlétisme Magazine and the athle.com website.
The sprinter himself seemed surprised by the honour.
"Are you sure it's me?" he said, reported sports daily L'Equipe.
"I haven't really done anything of note this year…I'm happy even if I'm not the only one who deserves this award."
Bernard Amsalem, the president of the FFA, said Lemaitre was popular with people across the board, particularly the young.
"He inspires an empathy and a simplicity….it makes him eminently sympathetic in the eyes of a large number of people," he said, adding that "children said they want to be like Christophe Lemaitre."