Eli Stowers attended John H. Guyer in Denton, Texas where he played quarterback. As a junior in 2019, he was the District 5-6A Co-Offensive MVP after passing for 2,969 yards with 36 touchdowns while adding 1,166 rushing yards and 11 touchdowns. Stowers also competed in track and field and won the 2019 Texas 6A high jump state title. He was rated a four-star prospect by 247Sports and committed to Texas A&M University.
Stowers dressed as a backup quarterback for five games in two seasons at Texas A&M without throwing a pass. After the 2022 season, Stowers entered the transfer portal and transferred to New Mexico State.
Stowers switched to tight end at New Mexico State and played 15 games in 2023. He finished the season with 35 receptions for 366 yards and two touchdowns while rushing for 108 yards and two touchdowns. He also completed 4 of 8 passes for 99 yards and one touchdown.
After the season, Stowers transferred for a second time, electing to play his senior season at Vanderbilt,