Lewtas has been promoted from coaching the Reds' U16s side to fill the role vacated by Steven Gerrard.
Academy director Alex Inglethorpe said: "We're delighted Barry has decided to take up this position.
"He already has a strong relationship with those players who will make the step up to our U18s in 2018-19 thanks to his previous role with the U16s."
Following Lewtas' move, Marc Bridge-Wilkinson has taken the post of Liverpool's U16s manager.