Smith, who suffered an ankle injury recently and will miss the remainder of the season, has made 32 appearances in all competitions this season.
The 26-year-old joined the Spireites from Yeovil on a two-year deal in June 2011.
"We're delighted that Nathan has agreed to stay because he's been in great form since I came here," said Paul Cook, who succeeded John Sheridan as manager in October.
The Liverpudlian also revealed that he has reached an agreement with an un-named striker to join the club.
He added: "Out of respect to the player and the club he's at, we're going to keep his identity under wraps at the moment."
Meanwhile, Manchester City winger Alex Henshall, 19, has had his loan spell at the Proact Stadium extended until the end of the season.