Jonathan Santucci comes from an athletic family. His father, Steven, attended Assumption College and played baseball there from 1991-1993 and his cousin, Nick, is currently attending Rollins College, where he also plays baseball. Jonathan attended Phillips Academy in Andover, Massachusetts, where he hit .322 over the course of his three year varsity career and showed a great deal of promise on the mound. One of the highest regarded prospects in the state of Massachusetts, he went undrafted in the 2021 MLB Draft and honored his commitment to Duke University.
Santucci appeared in 20 games in his freshman season, starting as a middle reliever but eventually transitioning and establishing himself as a weekend starting pitcher as the months went on.