Naquin attended Klein Collins High School, where he played for the school's baseball team. He lettered in baseball for three years. He was twice honored as All-State, three times honored as All-District, and three times named All-Greater Houston. Naquin grew up a Houston Astros fan.
The Cleveland Indians selected Naquin in the first round, with the 15th overall selection, of the 2012 Major League Baseball draft. He signed and made his professional debut that season with the Mahoning Valley Scrappers of the Rookie-levelNew York-Penn League, batting.270 in 36 games. Naquin played for the Carolina Mudcats of the Class A-AdvancedCarolina League and the Akron Aeros of the Class AAEastern League in 2013, hitting a combined.269 with ten home runs, 48 RBIs, and 15 stolen bases in 126 total games between both teams. After the 2013 season, the Indians assigned Naquin to the Arizona Fall League, and he participated in the Fall Stars Game. Naquin began the 2014 season with Akron, but suffered a broken hand in July. He required surgery, and missed the remainder of the 2014 season. In 76 games for Akron before his injury, he was batting.313 with four home runs and 30 RBIs. Naquin began the 2015 season with Akron. In June, the Indians promoted him to the Columbus Clippers of the Class AAAInternational League. However, a concussion and soreness in his right hip limited him to 50 games played with Columbus. In 84 games between Akron and Columbus, he slashed.300/.381/.446 with seven home runs and 27 RBIs. After the 2015 season, the Indians added Naquin to their 40-man roster. After the 2015 season, Naquin remained at the Indians' facility in Arizona to engage in strength training. He competed for a spot on the Indians' 25-man roster during spring training in 2016, and was named to the Opening Day roster. Naquin was named the American League Rookie of the Month for June and July 2016. On August 19, Naquin hit an inside-the-park home run to lead the Indians to a 3-2 win over the Toronto Blue Jays. He became the first Indians batter to hit a walk off inside-the-park home run since Braggo Roth, who accomplished the feat in 1916. In 116 games, he hit.296 with 14 home runs, 43 RBIs and 18 doubles. Naquin began 2017 with Cleveland. However, he was hampered with injuries and struggled with the Indians, and only appeared in 19 games for Cleveland in which he hit.216. He spent the majority of the year with Columbus where he slashed.298/.359/.475 with ten home runs and 51 RBIs in 80 games.