The 29-year-old, who took over the armband from Mark Fotheringham for the final 11 games of last term, will have summer signings Matt Gill and Michael Nelson as vice-captains.
Doherty, signed from Spurs five years ago, told the club's official website, "I'm delighted. It was something I wanted and I'm really pleased the manager has given it to me.
"I like to think I showed the right qualities last year and I think it upped my game too so that's a positive for my personal performances this season.
"It brings you out of your shell, it brings your game on and you want to be more dominant out on the pitch. That's what I want to do and bring on and I believe being captain will do that."