Benintendi attended Madeira High School in Madeira, Ohio. As a senior, he batted .564 with 12 home runs, 57 runs batted in (RBIs) and 38 stolen bases for the school's baseball team, and was the ABCA/Rawlings National High School Player of the Year and Ohio Gatorade Baseball Player of the Year. He finished his career with an Ohio record 199 career runs scored. Benintendi was drafted by the Cincinnati Reds in the 31st round of the 2013 Major League Baseball draft, but he did not sign with the Reds.

Benintendi enrolled at the University of Arkansas to play college baseball for the Arkansas Razorbacks baseball team. As a true freshman at Arkansas, Benintendi played in 61 games, with 60 starts. He hit .276/.368/.333 with one home run and 27 RBIs.

In 2015, Benintendi led the Southeastern Conference in batting average (.380), home runs (19), on-base percentage (.489), slugging (.715) and walks (47). He was named the SEC Player of the Year. He also won the Baseball America College Player of the Year Award, the Dick Howser Trophy, and the Golden Spikes Award. Benintendi was considered one of the top prospects for the 2015 Major League Baseball draft.