Clemens was selected by the New York Jets in the second round of the 2006 NFL Draft, the 49th overall pick, to serve as the secondary quarterback to Chad Pennington. A healthy Pennington resulted in little playing time for Clemens in 2006. He made his NFL debut in relief appearance against the Jacksonville Jaguars, recording his first career pass attempt and rushing once for two yards in the 41–0 loss. He entered in a Week 14 31–13 loss to the Buffalo Bills, rushed once for eight yards but did not attempt a pass. He recorded only two attempts and 0 completions in his rookie season.