Hilton committed to Florida International University (FIU) on February 6, 2008. He was scouted by the University of Mississippi, West Virginia University, the University of Florida and FIU. He made the choice to go to FIU over West Virginia the night before National Signing Day, when his son chose FIU eight times in a row when he put both an FIU and West Virginia hat in front of him.

Hilton was a starter under head coach Mario Cristobal in every year of his enrollment at FIU. In 2008, he returned a punt for a touchdown in his collegiate debut against Kansas on his first touch of the game. Later that year, in a game against Arkansas State, he threw a 38-yard touchdown pass to Junior Mertile late in the game after he fumbled the hand off in a reverse play. This play became known in FIU as “The Hilton Heave”. He was responsible for 12 touchdowns in his freshman year, scoring them all in five different ways, the first player in the program to do so (seven touchdown receptions, two rushing touchdowns, one passing touchdown, one punt return, and one kickoff return). He also set the FIU single season record for total receiving yards (41 receptions for 1,013 yards), average yards per reception (24.7 yards per reception), and all-purpose yardage (2,162). He finished his freshman season ranked third in the nation in all-purpose yardage per game, with an average of 180.25 yards per contest and was consequently named Sun Belt Freshman Player of the Year.

Foreshadowing the start of FIU’s 2009 campaign against Alabama, Crimson Tide head coach Nick Saban referred to Hilton as “a better offensive player than anybody [from Virginia Tech] that we played against last week”. In 2009, Hilton’s first touch of the season was a 96-yard kickoff return against Alabama. He paced the team with 57 catches for 632 yards and five touchdowns, as well as returning 22 kickoffs for 633 yards, despite struggling with an injured knee picked up in the fifth game of the season against the Western Kentucky Hilltoppers. He finished his sophomore season with 1,301 all-purpose yards.

In 2010, Hilton got off to a slow start, scoring no touchdowns in the first four games of the season, before returning home to play Western Kentucky and scoring his first touchdown of the season, a rushing touchdown. After a mid-season loss to the FAU Owls, Hilton came back strong the next game against the Louisiana-Monroe Warhawks, scoring four separate touchdowns, the first coming on a 95-yard kick return while the others were two passes from quarterback Wesley Carroll and the last a rushing touchdown. Later in the season against Troy, Hilton put up 158 yards rushing in six carries with two rushing touchdowns on his way to helping set a school record of 448 total rushing yards in a game.

In FIU’s first bowl game appearance in the 2010 Little Caesars Pizza Bowl, Hilton returned a kickoff for a touchdown in the second half of the game against the Toledo Rockets. He was also instrumental in a late hook and lateral play on a 4th-and-17 situation, helping his team get the first down and keeping them alive to eventually set up the winning field goal. He was named the Little Caesars Pizza Bowl MVP for his efforts in helping his team beat Toledo by a score of 34–32. At the end of his junior season, Hilton was honored as Sun Belt Player of the Year, as well as being named to the All-Sun Belt Conference First Team at the wide receiver and return specialist positions. He finished his junior season with 2,089 all-purpose yards, 848 of them on receptions over 59 catches and 282 rushing yards over 30 carries, a personal best.

In 2011, Hilton got off to a hot start in his senior season, putting up a school record 283 all-purpose yards in FIU’s rout of the North Texas Mean Green. A week later, Hilton was instrumental in FIU’s 24–17 upset of the Louisville Cardinals, with 74 and 83 yard catches for touchdowns. He finished that game with seven receptions for 201 yards, breaking his school and personal single game receiving records.

On April 27, 2012, Hilton was selected in the third round with the 92nd overall pick of the 2012 NFL Draft by the Indianapolis Colts. He was the 13th wide receiver taken in the draft. In late May 2012, Hilton signed a contract with Indianapolis worth $2.6 million over four years. Hilton was utilized during his rookie season as a punt/kick returner and as a slot receiver for fellow rookie, quarterback Andrew Luck. During a Week 12 game against the Buffalo Bills, Hilton returned a punt for 75 yards and later caught an eight-yard touchdown pass. The two scores proved to be the difference in a 20–13 victory.

Hilton and his wife, Shantrell, had a baby girl on November 23, 2014. He also has a son named Eugene Jr. Hilton, whose given name is Eugene, explained how he became known as T. Y.: “My daddy’s name is Tyrone, so ever since I was little, everyone has just used the first two letters of that.”

On August 13, 2015, Hilton signed a five-year, $65 million extension with the Colts, with $39 million guaranteed. He played in all 16 games in the 2015 season, recording 69 receptions for 1,124 yards and five touchdowns. On January 25, 2016, Hilton was named to his second-consecutive Pro Bowl.

In Week 3 against the Cleveland Browns, Hilton caught seven passes for 153 yards and a 61-yard touchdown to help the Colts win 31–28. In Week 5 against the San Francisco 49ers, Hilton caught seven passes for 177 yards to help the Colts win 26–23 in overtime. During Week 9 against the Houston Texans, Hilton posted an NFL-leading 175 receiving yards and two touchdowns as the Colts won 20–14, earning him AFC Offensive Player of the Week. He finished the season with 57 receptions for 966 yards and four touchdowns. He was named to his fourth straight Pro Bowl on January 10, 2018, as an injury replacement.

Hilton was placed on the active/non-football injury list at the start of training camp on August 2, 2020. He was added back to the active roster on August 12.