"Tate Wallis has offered his resignation and we have accepted it," the school said Thursday.
Wallis was hired at North Texas in January. The allegations stem from his time as the offensive coordinator at Argyle High School near Denton, Texas.
Argyle ISD's police department said the investigation began in March after multiple Argyle students reported alleged inappropriate behavior by Wallis in 2018 and 2019. The two counts are felonies in Texas.
Wallis' attorney, Stephanie Luce Ola, issued a statement Thursday after his resignation.
"Coach Wallis is very grateful for the support he has received from the community. He has stepped down from his position at UNT to focus on his family and on defending the allegations that have been made against him," the statement said. "He doesn't want his upcoming legal battle to be a distraction for the team and wishes them the best in this upcoming season."
Prior to North Texas, Wallis was an assistant from 2009 to 2015 at Baylor under Art Briles. He then spent spent four years as a high school coach at North Forney and Argyle.