Cook served as the Big Green's head coach for 12 years and posted an overall record of 106-74-31 while leading his squad to five Ivy League titles and seven NCAA Tournament appearances.
"We are deeply grateful for the profound impact Jeff has had on our program and on the lives of his student-athletes," said Dartmouth Athletics Director Harry Sheehy. "We at Dartmouth wish him many years of success at the professional level. Jeff will always be a member of the Big Green family."
Cook said: "This coaching position with the Philadelphia Union Youth Academy is very exciting and I look forward to working with the club in their efforts to develop an outstanding youth development academy. The Union are incredibly committed to youth development, and that message shone through as I learned more about their plans and the specific nature of my role. I believe passionately in the quality of the American youth player, and the Union will provide a pathway for some of the most outstanding youth players in the country to progress towards the elite level of our sport."