Scott ended last season as caretaker manager of the club, following Neale Cooper's shock exit, and led the club to the League One play-off final, only for them to be defeated by Sheffield Wednesday after extra time.
Scott appointed as Hartlepool boss
But the new manager feels there are solid foundations at the club, where he has been a coach for three years.
"This is the right time for me and I think the chairman and I have made the right decision," said Scott.
"We know how far the club has come in recent years and it is important that we keep moving forward and progressing.
"I was very naive when I first came to the club but I have learnt and I am not afraid to admit that - I have learnt to think like a manager and although I have things still to improve on I am really excited to get this chance."
He added: "I know the players will be looking forward to next season and they know the standards I will be expecting of them will be really high."