The Vanarama National League North side announced Dean's departure on Saturday evening after he missed their 2-1 defeat to Kidderminster Harriers.
Dean brings long-serving assistant manager Chris Plummer with him with former Iron interim boss Michael Nelson staying on as head coach.
A tough first half of the season has seen Scunthorpe struggle, finding themselves second-bottom of the Vanarama National League.
Dean arrives with results stabilised - with the Iron losing just once in their last four outings.
First up for Dean is Friday night's home game with Barnet before a crunch relegation battle with Maidstone a week later.