The 46-year-old, who arrived from Accrington Stanley in October 2012, has extended his terms with the Spireites until 2016.
Chesterfield are currently at the top of the table thanks to their unbeaten start to the season.
"From the chairman down, everyone here has been really supportive," Cook told the club's official website.
"They gave me an opportunity to manage such a great club and the least I can do is repay their faith in me by signing a new deal."
Chesterfield are back in league action on Saturday when they host fifth-placed Mansfield Town.