Compher replaced Terry Holland, who announced his retirement earlier this year.
"Jeff Compher is a proven leader in moving an entire athletic department forward," said ECU Chancellor Steve Ballard. "He has great values, great experience, and national recognition among his peers. We are delighted he is a Pirate."
According to East Carolina, Compher is a Baltimore native and attended James Madison University. He started his career at N.C. State, spending 13 years in various roles. Compher was at NIU since 2008.
"I would like to thank the search committee, the members of the Board of Trustees, and especially Chancellor Ballard for this outstanding opportunity to lead the ECU Athletics Department," Compher said.
Compher will receive an annual salary of $415,000, along with bonuses for athletic, academic and compliance performance by the program.
The East Carolina Educational Foundation, known as the Pirate Club, will partially fund the salary along with other non-state appropriated funds.