West Virginia
On April 6, 2016, Grier announced that he was transferring to West Virginia University. He sat out the 2016 season per NCAA transfer rules. Grier was the presumed starter for West Virginia heading into the 2017 season, but there were questions surrounding his eligibility, since half of his year-long suspension was served in conjunction with his transfer waiting period. On June 20, 2017, West Virginia head coach Dana Holgerson announced that the NCAA had granted Grier a waiver and he would be eligible to play in the season opener against Virginia Tech. In his first game with the Mountaineers, Grier threw for 371 yards, three touchdowns and an interception in a 31–24 loss to Virginia Tech. Grier threw for 352 yards and five touchdowns in a come-from-behind victory over then-No. 24 Texas Tech on October 14, and was named Big 12 Offensive Player of the Week. In the Mountaineers’ 11th game of the season, against Texas, Grier left the game in the second quarter with a broken finger on his throwing hand. Grier had surgery on the broken finger and missed the remainder of the season, finishing with 3,490 passing yards and 36 total touchdowns on the year. At the conclusion of the season, Grier was awarded as Big 12 Offensive Newcomer of the Year.
On December 14, 2017, Grier announced he would be returning for his senior season rather than entering the 2018 NFL draft. He was listed on preseason watch lists for several national awards, including the Maxwell Award, Walter Camp Award, and Davey O'Brien Award. Grier appeared in several preseason lists of potential Heisman Trophy candidates. At the 2018 Big 12 Media Days, he was announced as the conference's Preseason Offensive Player of the Year and a preseason first-team all-conference selection.
Grier finished the 2018 season with 3,864 passing yards, 37 touchdowns, and eight interceptions. He was named second-team All-Big 12 at the conclusion of the regular season. West Virginia finished with an 8–3 regular season record and was invited to the Camping World Bowl; Grier announced that he would not play in the bowl game, in order to prepare for the 2019 NFL draft. Grier would be named the winner of the 2018 Senior CLASS Award for FBS football as the outstanding senior student-athlete in that grouping of schools.