West, who made 147 appearances for City during two spells at Sincil Bank, enjoyed a successful playing career notably at Burnley and Bury, and had previously been coaching part-time in both the schoolboy and youth programme.
He will be working day-to-day with the youth team as well as overseeing the development of the under-16 squad.
"I'm really looking forward to the challenge ahead and to working every day on the training ground at the club which gave me my first opportunity in football," he said.
Commenting on the appointment, academy manager Damian Froggatt said: "Dean has been coaching in the academy for almost three years now and we are delighted to have secured his appointment on a more permanent basis.
"Not only does he bring a wealth of playing experience with him, he is also passionate about Lincoln City and about the development of its young players."
West takes up his post with immediate effect.