The 26-year-old, who made 52 appearances in total for the Bantams last season, will remain with the club throughout the 2013/14 League One campaign.
Manager Phil Parkinson told the club's official website: "I'm obviously delighted Nathan has signed on with us again for next season.
"He was a key performer in the side last season and adds versatility and quality to the squad.
"Having joined us just before the very start of the season last year, the beauty is that this time around we have him in the building for the whole of pre-season.
"Hopefully that means we can get even more out of him this season."
Doyle started his career at Derby and moved on to Hull in 2007, but made a big impact when switching to Barnsley, initially on loan, in 2009.
He made over 80 appearances for the Tykes and following a loan spell at Preston joined Bradford at the start of last season.