In the space of 11 months, Flynn has transformed Newport into promotion contenders after initially taking over when the Welsh club were battling for survival at the fourth tier.
The announcement comes on the same day as Newport's FA Cup fourth-round replay with Tottenham Hotspur at Wembley Stadium, and Flynn has acknowledged that he jumped at the chance to extend his contract until 2020.
The 37-year-old told the club's official website: "I'm delighted that the board have agreed to improve my current deal.
"I've always said I want to build a Club and not a team and the increase in my tenure helps achieve that goal."
Flynn has recorded 23 wins and 12 draws from his 52 matches in charge.