The former Wales Under-21 coach claimed earlier today that he was open to taking the full-time role after being named as the caretaker boss following Dean Saunders's departure.
"I am delighted to have received the news from the chairman and board of directors this afternoon," Flynn told the club's official website.
"Continuity is key. I've been here six months and in charge [for] 10 days and nothing is broken so nothing needs to change.
"When you walk into a dressing room, you can tell there is success in the air, and that's the feeling I got when I came down to the training ground at Cantley Park. I could sense that the players were hungry for success."
Player-coach Rob Jones has been named as Flynn's assistant manager.